Variant report

Variant	rs3741378
Chromosome Location	chr11:65408937-65408938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65408817-65409211	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:65406836-65409035	GM12892	blood:	n/a	n/a
3	ELF1	chr11:65407022-65409231	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:65408613-65409048	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:65406835-65409596	GM12892	blood:	n/a	n/a
6	POLR2A	chr11:65406957-65408993	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:65408817-65409988	GM12892	blood:	n/a	n/a
8	MTA3	chr11:65408685-65409688	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:65404870-65410346	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:65406961-65409167	HL-60	blood:	n/a	n/a
11	POLR2A	chr11:65408467-65410150	K562	blood:	n/a	n/a
12	EBF1	chr11:65406936-65408947	GM12878	blood:	n/a	chr11:65407865-65407874 chr11:65407820-65407831 chr11:65407865-65407875 chr11:65407864-65407875 chr11:65407822-65407831
13	STAT1	chr11:65408916-65409007	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65408028..65411075-chr11:65624392..65627555,3	K562	blood:
2	chr11:65380696..65385200-chr11:65403578..65408941,10	MCF-7	breast:
3	chr11:65341380..65343609-chr11:65408104..65410405,2	MCF-7	breast:
4	chr11:65395794..65396338-chr11:65408470..65409118,2	MCF-7	breast:
5	chr11:65408552..65410690-chr11:65624171..65626866,2	K562	blood:

Variant related genes	Relation type
SIPA1	TF binding region
ENSG00000172732	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000173327	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11227247	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs12417989	0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs12418567	0.81[EUR][1000 genomes]
rs12418630	0.87[EUR][1000 genomes]
rs12418683	0.85[EUR][1000 genomes]
rs12419110	0.88[EUR][1000 genomes]
rs12420618	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12421691	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs1962691	0.89[EUR][1000 genomes]
rs1963977	0.81[EUR][1000 genomes]
rs2075660	0.95[EUR][1000 genomes]
rs2127510	0.81[EUR][1000 genomes]
rs2306365	0.93[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs35927673	0.89[EUR][1000 genomes]
rs36028748	0.87[EUR][1000 genomes]
rs36091060	0.81[EUR][1000 genomes]
rs36113281	0.87[EUR][1000 genomes]
rs3782086	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4578394	0.81[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap]
rs4645916	0.81[EUR][1000 genomes]
rs4930158	0.89[EUR][1000 genomes]
rs4930299	0.87[EUR][1000 genomes]
rs56115979	0.89[EUR][1000 genomes]
rs7101916	0.93[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs7107503	0.81[EUR][1000 genomes]
rs7119750	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs7122081	0.81[EUR][1000 genomes]
rs7122098	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
4	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
5	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
6	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
8	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
9	nsv468599	chr11:65335705-65427346	ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv555213	chr11:65335705-65427346	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
11	nsv897732	chr11:65335705-65427346	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
12	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
14	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
15	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
16	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
17	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
18	nsv897746	chr11:65349756-65427346	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
19	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
20	esv1831135	chr11:65387352-65420872	Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	43 gene(s)	inside rSNPs	diseases
21	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
22	nsv897749	chr11:65401748-65420760	Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	39 gene(s)	inside rSNPs	diseases
23	nsv897750	chr11:65401748-65421476	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
24	nsv897751	chr11:65401748-65425167	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
25	nsv897752	chr11:65405300-65421476	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
26	nsv897753	chr11:65405300-65422693	Genic enhancers Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
27	nsv897754	chr11:65405300-65436888	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
28	nsv897755	chr11:65405300-65481166	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
29	nsv897756	chr11:65406393-65425167	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
30	nsv897757	chr11:65406393-65427568	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3741378	SF3B2	cis	cerebellum	SCAN
rs3741378	PRDX5	cis	parietal	SCAN
rs3741378	C11orf2	cis	cerebellum	SCAN
rs3741378	PLA2G16	cis	parietal	SCAN
rs3741378	GPHA2	cis	parietal	SCAN
rs3741378	MALAT1	cis	parietal	SCAN
rs3741378	MALAT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65405200-65409600	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr11:65405200-65409600	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr11:65405800-65409800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:65406000-65409000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr11:65406000-65409200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:65406000-65409800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr11:65406200-65409600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr11:65406200-65409600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr11:65406400-65409000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:65406400-65409400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:65406400-65409400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:65406400-65409400	Weak transcription	Fetal Brain Female	brain
13	chr11:65406400-65413000	Weak transcription	Fetal Heart	heart
14	chr11:65406400-65414600	Weak transcription	Ovary	ovary
15	chr11:65406400-65416800	Weak transcription	Aorta	Aorta
16	chr11:65406600-65409000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:65406600-65409000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:65406600-65409000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:65406600-65409000	Weak transcription	Brain Angular Gyrus	brain
20	chr11:65406600-65409200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:65406600-65409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:65406600-65409200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:65406600-65409200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:65406600-65409200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr11:65406600-65409200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:65406600-65409200	Weak transcription	Fetal Intestine Large	intestine
27	chr11:65406600-65409400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:65406600-65409400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:65406600-65409400	Weak transcription	Brain Germinal Matrix	brain
30	chr11:65406600-65409600	Enhancers	Left Ventricle	heart
31	chr11:65406600-65409600	Weak transcription	NH-A	brain
32	chr11:65406600-65410600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:65406600-65410800	Weak transcription	A549	lung
34	chr11:65406600-65410800	Weak transcription	Hela-S3	cervix
35	chr11:65406600-65411200	Weak transcription	HepG2	liver
36	chr11:65406600-65411400	Weak transcription	HMEC	breast
37	chr11:65406600-65412800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:65406600-65412800	Weak transcription	HSMMtube	muscle
39	chr11:65406600-65414400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:65406600-65414400	Weak transcription	NHEK	skin
41	chr11:65406600-65414600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:65406600-65414600	Weak transcription	Osteobl	bone
43	chr11:65406600-65419200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:65407000-65409000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr11:65407000-65409600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:65407000-65415000	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr11:65407200-65409200	Enhancers	Right Atrium	heart
48	chr11:65407200-65409400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:65407200-65410000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:65407200-65410200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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