Variant report

Variant	rs11608756
Chromosome Location	chr12:889833-889834
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	EP300	chr12:889319-890093	ECC-1	luminal epithelium:	n/a	n/a
2	CUX1	chr12:889765-889908	GM12878	blood:	n/a	n/a
3	TEAD4	chr12:889334-889993	ECC-1	luminal epithelium:	n/a	n/a
4	JUND	chr12:888826-889914	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr12:888791-890004	SK-N-SH	brain:	n/a	n/a
6	TBL1XR1	chr12:889808-889877	GM12878	blood:	n/a	n/a
7	FOSL2	chr12:888805-889917	SK-N-SH	brain:	n/a	n/a
8	TEAD4	chr12:889317-889947	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr12:888950-889989	SK-N-SH	brain:	n/a	chr12:889440-889461 chr12:889308-889321
10	TEAD4	chr12:889371-889966	ECC-1	luminal epithelium:	n/a	n/a
11	EP300	chr12:889791-889945	GM12878	blood:	n/a	n/a
12	NFIC	chr12:889139-889988	SK-N-SH	brain:	n/a	n/a
13	EP300	chr12:889817-890376	GM12878	blood:	n/a	n/a
14	PBX3	chr12:889139-890034	SK-N-SH	brain:	n/a	n/a
15	MAX	chr12:889428-889903	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
RNU4ATAC16P	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10774458	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10774465	0.81[ASN][1000 genomes]
rs10774467	0.81[ASN][1000 genomes]
rs10849559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10849560	0.81[ASN][1000 genomes]
rs10849561	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs10849563	0.86[JPT][hapmap]
rs10849564	0.81[ASN][1000 genomes]
rs11064560	0.88[JPT][hapmap]
rs11064575	0.81[ASN][1000 genomes]
rs1159744	0.88[JPT][hapmap]
rs11615237	0.81[ASN][1000 genomes]
rs2107612	0.86[JPT][hapmap]
rs2107613	0.86[JPT][hapmap]
rs2158501	0.81[ASN][1000 genomes]
rs2158502	0.86[JPT][hapmap]
rs2240284	0.81[ASN][1000 genomes]
rs2369402	0.88[JPT][hapmap]
rs6489756	0.81[ASN][1000 genomes]
rs7137311	0.81[ASN][1000 genomes]
rs727880	0.81[ASN][1000 genomes]
rs7298426	0.89[ASN][1000 genomes]
rs7305065	0.81[ASN][1000 genomes]
rs7311290	0.81[ASN][1000 genomes]
rs7311746	0.81[ASN][1000 genomes]
rs7314017	0.81[ASN][1000 genomes]
rs765250	0.86[JPT][hapmap]
rs7959509	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
8	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
9	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
10	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
11	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv898568	chr12:547683-969800	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS 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 target site	58 gene(s)	inside rSNPs	diseases
14	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
15	nsv1051590	chr12:722215-974773	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
16	nsv541338	chr12:722215-974773	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv468956	chr12:737230-982321	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv556893	chr12:737230-982321	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	esv2757485	chr12:786238-964551	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
20	nsv1046707	chr12:792110-910520	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
21	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
22	esv2754685	chr12:835074-936468	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
23	esv2753750	chr12:835074-939480	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
24	esv2753658	chr12:835074-964506	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
25	esv3693103	chr12:837113-971317	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
26	nsv556898	chr12:850288-968489	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
27	nsv468959	chr12:850613-922408	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
28	nsv556899	chr12:850613-922408	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
29	nsv518946	chr12:854331-961336	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
30	nsv556900	chr12:854331-968489	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
31	esv2752382	chr12:863833-964506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
32	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
33	esv1840640	chr12:866857-898400	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	nsv898577	chr12:873890-969800	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
35	nsv898578	chr12:876288-909731	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11608756	WNK1,HSN2	cis	brain	BrainEAC
rs11608756	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:865200-895600	Weak transcription	Pancreas	Pancrea
2	chr12:881800-891400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:883600-905200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:883800-923200	Weak transcription	Fetal Stomach	stomach
5	chr12:884000-891600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:884800-891600	Enhancers	Brain Hippocampus Middle	brain
7	chr12:884800-899000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:885200-890600	Enhancers	Brain Substantia Nigra	brain
9	chr12:885200-896000	Weak transcription	Dnd41	blood
10	chr12:885400-891800	Weak transcription	Fetal Thymus	thymus
11	chr12:885400-897000	Weak transcription	Fetal Intestine Small	intestine
12	chr12:885400-898400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:885400-904000	Weak transcription	Thymus	Thymus
14	chr12:885600-890000	Enhancers	Stomach Mucosa	stomach
15	chr12:885600-892000	Weak transcription	Ovary	ovary
16	chr12:886000-895800	Weak transcription	Lung	lung
17	chr12:886200-890600	Enhancers	Colon Smooth Muscle	Colon
18	chr12:886200-891600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr12:886600-890000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr12:886600-891400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr12:886600-895600	Weak transcription	Left Ventricle	heart
22	chr12:886800-890600	Enhancers	HepG2	liver
23	chr12:887000-890400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:887600-890400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:887800-890000	Enhancers	NHEK	skin
26	chr12:887800-890400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:887800-890600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr12:887800-891800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:887800-895600	Weak transcription	Esophagus	oesophagus
30	chr12:888000-890200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:888000-890400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:888000-890400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr12:888000-891400	Enhancers	Hela-S3	cervix
34	chr12:888200-890800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:888200-891600	Enhancers	Fetal Heart	heart
36	chr12:888400-890600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr12:888400-892200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:888600-890000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:888600-890200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:888600-890200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:888600-890400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr12:888600-890800	Enhancers	Adipose Nuclei	Adipose
43	chr12:888800-890000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:888800-890000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:888800-890000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr12:888800-890400	Enhancers	Fetal Lung	lung
47	chr12:888800-890400	Enhancers	HMEC	breast
48	chr12:888800-890600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:888800-890600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr12:888800-890600	Flanking Active TSS	GM12878-XiMat	blood

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