Variant report

Variant	rs10838702
Chromosome Location	chr11:47410888-47410889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr11:47410454-47411053	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:47409305-47412146	HL-60	blood:	n/a	n/a
3	POLR2A	chr11:47409409-47413887	HL-60	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47400738..47402278-chr11:47408307..47410990,2	MCF-7	breast:
2	chr11:47395359..47404298-chr11:47408556..47417905,22	K562	blood:
3	chr11:47399283..47402217-chr11:47408896..47411189,2	K562	blood:
4	chr11:47408757..47411550-chr11:47413345..47415143,3	K562	blood:
5	chr11:47407132..47409487-chr11:47410035..47412468,2	K562	blood:
6	chr11:47398614..47400685-chr11:47410760..47413016,2	MCF-7	breast:
7	chr11:47410723..47415239-chr11:47428368..47430840,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000265910	TF binding region
ENSG00000255197	Chromatin interaction
ENSG00000066336	Chromatin interaction
ENSG00000265910	Chromatin interaction
ENSG00000165915	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10437655	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10742802	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10742814	0.84[GIH][hapmap]
rs10769263	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769264	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838705	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838709	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10838726	0.94[CHB][hapmap]
rs11039221	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039225	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039244	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs11606287	0.92[CEU][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs12292911	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1377416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1534576	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242081	0.84[GIH][hapmap]
rs2278890	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2293576	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs2293579	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34937994	0.82[EUR][1000 genomes]
rs35032070	0.90[EUR][1000 genomes]
rs3740699	0.84[GIH][hapmap]
rs3758675	0.86[EUR][1000 genomes]
rs3824869	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4434960	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61897431	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6485758	0.88[CHB][hapmap]
rs7103648	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7104036	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7933019	0.94[CHB][hapmap]
rs7947450	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs874896	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs896817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic 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	38 gene(s)	inside rSNPs	diseases
8	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10838702	C1QTNF4	cis	lymphoblastoid	seeQTL
rs10838702	C1QTNF4	cis	multi-tissue	Pritchard
rs10838702	MADD	cis	parietal	SCAN
rs10838702	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10838702	MTCH2	cis	cerebellum	SCAN

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47399400-47421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:47399800-47421200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:47400000-47415200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:47400000-47416000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:47400000-47416800	Weak transcription	Brain Anterior Caudate	brain
6	chr11:47400000-47421200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr11:47404400-47412800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:47405000-47412800	Weak transcription	K562	blood
9	chr11:47405400-47415000	Weak transcription	Right Atrium	heart
10	chr11:47408400-47418000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr11:47408600-47416000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:47409200-47417800	Enhancers	Spleen	Spleen
13	chr11:47409400-47411200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:47409400-47411600	Enhancers	Esophagus	oesophagus
15	chr11:47409400-47414200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:47409400-47414400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:47409400-47415000	Enhancers	Primary hematopoietic stem cells	blood
18	chr11:47409600-47411000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:47409600-47411000	Enhancers	HMEC	breast
20	chr11:47409600-47411600	Enhancers	Placenta	Placenta
21	chr11:47409600-47412000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr11:47409600-47415800	Enhancers	Adipose Nuclei	Adipose
23	chr11:47409800-47411000	Enhancers	Primary B cells from cord blood	blood
24	chr11:47409800-47411200	Enhancers	Fetal Muscle Trunk	muscle
25	chr11:47409800-47417600	Enhancers	Fetal Muscle Leg	muscle
26	chr11:47410000-47411000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr11:47410000-47411000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:47410000-47411200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:47410000-47411400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr11:47410000-47412200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr11:47410000-47412600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr11:47410000-47416800	Weak transcription	Brain Substantia Nigra	brain
33	chr11:47410200-47411000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:47410200-47411000	Weak transcription	Fetal Thymus	thymus
35	chr11:47410200-47412800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr11:47410200-47421200	Weak transcription	Fetal Intestine Small	intestine
37	chr11:47410400-47411000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr11:47410400-47412000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr11:47410600-47411000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr11:47410600-47411000	Enhancers	HepG2	liver
41	chr11:47410600-47411000	Enhancers	NHEK	skin
42	chr11:47410600-47411800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr11:47410600-47412000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr11:47410600-47415800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:47410800-47411200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr11:47410800-47411800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr11:47410800-47412000	Enhancers	Primary T cells from cord blood	blood
48	chr11:47410800-47412400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:47410800-47413000	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:47410800-47415600	Weak transcription	Gastric	stomach

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