Variant report

Variant	rs3781579
Chromosome Location	chr11:68209718-68209719
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	KAP1	chr11:68209066-68209817	HEK293	kidney:	n/a	n/a
2	KAP1	chr11:68208914-68210251	U2OS	brain:	n/a	n/a
3	EP300	chr11:68209340-68209765	SK-N-SH_RA	brain:	n/a	n/a
4	EP300	chr11:68208863-68209824	ECC-1	luminal epithelium:	n/a	chr11:68209123-68209137
5	YY1	chr11:68209374-68209785	SK-N-SH_RA	brain:	n/a	n/a
6	GATA2	chr11:68209018-68210303	SH-SY5Y	brain:	n/a	chr11:68209125-68209135
7	YY1	chr11:68209482-68209718	SK-N-SH_RA	brain:	n/a	n/a
8	EP300	chr11:68208579-68209855	SK-N-SH	brain:	n/a	chr11:68209123-68209137
9	GATA3	chr11:68209556-68210306	SH-SY5Y	brain:	n/a	n/a
10	POLR2A	chr11:68209356-68209731	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:68209498..68212492-chr11:68216141..68219004,3	K562	blood:
2	chr11:68204961..68210848-chr11:68212670..68216087,6	K562	blood:
3	chr11:67980477..67985206-chr11:68208162..68213238,5	MCF-7	breast:
4	chr11:68206590..68210286-chr11:68212679..68215708,3	K562	blood:

Variant related genes	Relation type
LRP5	TF binding region
ENSG00000162337	Chromatin interaction
ENSG00000110066	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11228271	1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs12363572	0.84[CHD][hapmap];1.00[MEX][hapmap]
rs2242340	0.80[EUR][1000 genomes]
rs2510375	1.00[MEX][hapmap]
rs73516825	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347272	chr11:67969427-68218997	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
2	nsv897857	chr11:68056770-68231240	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897858	chr11:68077238-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv897859	chr11:68102000-68231240	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv897860	chr11:68102000-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1047532	chr11:68103330-68239242	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv541082	chr11:68103330-68239242	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1036561	chr11:68123135-68315685	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv897862	chr11:68129606-68236389	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv469965	chr11:68140781-68217420	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv555285	chr11:68144283-68231240	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv468618	chr11:68171013-68231240	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv897863	chr11:68186392-68251460	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	nsv520841	chr11:68199008-68217420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv1792339	chr11:68199008-68299226	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	esv1803199	chr11:68199008-68299226	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	esv1842405	chr11:68199008-68299226	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv526402	chr11:68201295-68217420	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3781579	TPCN2	cis	parietal	SCAN
rs3781579	SPTBN2	cis	parietal	SCAN
rs3781579	SHANK2	cis	cerebellum	SCAN
rs3781579	DNAJC4	cis	cerebellum	SCAN
rs3781579	RIN1	cis	parietal	SCAN
rs3781579	C11orf85	cis	parietal	SCAN
rs3781579	AIP	cis	cerebellum	SCAN
rs3781579	FOSL1	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68176000-68210400	Strong transcription	HepG2	liver
2	chr11:68182800-68222200	Weak transcription	Small Intestine	intestine
3	chr11:68197400-68210600	Strong transcription	Dnd41	blood
4	chr11:68197400-68214400	Strong transcription	Fetal Intestine Small	intestine
5	chr11:68197400-68214600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:68197400-68214800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr11:68197400-68216400	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr11:68197400-68217800	Strong transcription	Liver	Liver
9	chr11:68197600-68210800	Strong transcription	Brain Germinal Matrix	brain
10	chr11:68197600-68217800	Strong transcription	Fetal Intestine Large	intestine
11	chr11:68197600-68227000	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:68198200-68210600	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:68198600-68215000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:68198800-68227000	Weak transcription	Brain Anterior Caudate	brain
15	chr11:68199600-68210600	Strong transcription	Colonic Mucosa	Colon
16	chr11:68200600-68210200	Strong transcription	Primary T cells from cord blood	blood
17	chr11:68201000-68227400	Weak transcription	Fetal Brain Male	brain
18	chr11:68201600-68218800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:68205000-68210600	Strong transcription	Gastric	stomach
20	chr11:68205200-68210200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:68205200-68210800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr11:68205400-68210600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:68205400-68210600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:68205400-68210600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:68205400-68210800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:68205400-68218000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:68205600-68215200	Weak transcription	K562	blood
28	chr11:68205600-68215400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:68205800-68212000	Weak transcription	HUVEC	blood vessel
30	chr11:68205800-68215800	Weak transcription	HMEC	breast
31	chr11:68206000-68210600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:68206000-68210600	Strong transcription	Left Ventricle	heart
33	chr11:68206000-68214600	Strong transcription	Lung	lung
34	chr11:68206200-68210000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:68206400-68210000	Genic enhancers	Fetal Stomach	stomach
36	chr11:68206600-68210400	Strong transcription	Right Ventricle	heart
37	chr11:68206600-68210600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:68206800-68209800	Genic enhancers	Placenta	Placenta
39	chr11:68206800-68210400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:68206800-68214400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:68206800-68227200	Weak transcription	Fetal Kidney	kidney
42	chr11:68207000-68210000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr11:68207000-68210400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr11:68207000-68210400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:68207000-68210400	Enhancers	Fetal Lung	lung
46	chr11:68207000-68214400	Weak transcription	Stomach Mucosa	stomach
47	chr11:68207000-68214800	Weak transcription	Aorta	Aorta
48	chr11:68207000-68227400	Weak transcription	Brain Substantia Nigra	brain
49	chr11:68207200-68209800	Enhancers	HSMMtube	muscle
50	chr11:68207200-68214400	Weak transcription	Fetal Thymus	thymus

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