Variant report

Variant	rs669556
Chromosome Location	chr11:85781322-85781323
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	chr11:85779071-85781362	GM19099	blood:	n/a	n/a
2	PBX3	chr11:85779790-85781881	SK-N-SH	brain:	n/a	chr11:85781807-85781816 chr11:85781678-85781689
3	ZNF143	chr11:85779909-85781401	GM12878	blood:	n/a	chr11:85780270-85780280
4	NFYB	chr11:85780047-85781363	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:85775966-85781389	Hela-S3	cervix:	n/a	n/a
6	STAT3	chr11:85780434-85781428	GM12878	blood:	n/a	n/a
7	CREB1	chr11:85779899-85781362	K562	blood:	n/a	n/a
8	TEAD4	chr11:85777972-85781354	K562	blood:	n/a	n/a
9	GTF2F1	chr11:85779990-85781427	Hela-S3	cervix:	n/a	n/a
10	MTA3	chr11:85778924-85781339	GM12878	blood:	n/a	n/a
11	TCF12	chr11:85779742-85782012	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr11:85780396-85781426	GM12878	blood:	n/a	n/a
13	MAX	chr11:85778179-85781459	NB4	blood:	n/a	chr11:85780346-85780365 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780042-85780052 chr11:85780162-85780181 chr11:85780805-85780816 chr11:85780349-85780362 chr11:85780350-85780361 chr11:85780165-85780178
14	EP300	chr11:85779706-85781401	ECC-1	luminal epithelium:	n/a	chr11:85780271-85780280 chr11:85781025-85781039 chr11:85781026-85781035
15	MEF2A	chr11:85779911-85781326	SK-N-SH	brain:	n/a	chr11:85780856-85780871 chr11:85780852-85780873
16	POLR2A	chr11:85779102-85781413	HUVEC	blood vessel:	n/a	n/a
17	SMC3	chr11:85780070-85781360	GM12878	blood:	n/a	n/a
18	MAX	chr11:85778878-85781445	GM12878	blood:	n/a	chr11:85780346-85780365 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780042-85780052 chr11:85780162-85780181 chr11:85780805-85780816 chr11:85780349-85780362 chr11:85780350-85780361 chr11:85780165-85780178
19	SPI1	chr11:85780540-85781353	GM12878	blood:	n/a	chr11:85780939-85780952 chr11:85781030-85781039
20	POLR2A	chr11:85780686-85781365	HepG2	liver:	n/a	n/a
21	RFX5	chr11:85778655-85781378	IMR90	lung:	n/a	n/a
22	TCF12	chr11:85779826-85781342	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr11:85778959-85781377	HCT-116	colon:	n/a	chr11:85780346-85780365 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780042-85780052 chr11:85780162-85780181 chr11:85780805-85780816 chr11:85780349-85780362 chr11:85780350-85780361 chr11:85780165-85780178
24	SRF	chr11:85780680-85781325	ECC-1	luminal epithelium:	n/a	chr11:85781022-85781036 chr11:85781018-85781036 chr11:85781020-85781033
25	RELA	chr11:85779955-85781433	GM10847	blood:	n/a	n/a
26	MYC	chr11:85779470-85781357	K562	blood:	n/a	chr11:85780346-85780365 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780042-85780052 chr11:85780162-85780181 chr11:85780805-85780816 chr11:85780349-85780362 chr11:85780350-85780361 chr11:85780165-85780178
27	EP300	chr11:85780670-85781373	Hela-S3	cervix:	n/a	chr11:85781025-85781039 chr11:85781026-85781035
28	BRCA1	chr11:85780020-85781445	Hela-S3	cervix:	n/a	n/a
29	CHD1	chr11:85776392-85781605	IMR90	lung:	n/a	n/a
30	POLR2A	chr11:85779041-85781333	GM12892	blood:	n/a	n/a
31	POLR2A	chr11:85778175-85781459	Hela-S3	cervix:	n/a	n/a
32	JUND	chr11:85780664-85781388	Hela-S3	cervix:	n/a	chr11:85780991-85781002 chr11:85781028-85781037
33	POLR2A	chr11:85779067-85781341	GM12878	blood:	n/a	n/a
34	NFIC	chr11:85779977-85781481	GM12878	blood:	n/a	n/a
35	TBP	chr11:85779971-85781426	GM12878	blood:	n/a	n/a
36	FOS	chr11:85780558-85781325	HUVEC	blood vessel:	n/a	chr11:85780991-85781002 chr11:85781028-85781037
37	JUN	chr11:85780760-85781341	K562	blood:	n/a	chr11:85780991-85781002 chr11:85781028-85781037
38	POLR2A	chr11:85778968-85781327	GM12892	blood:	n/a	n/a
39	POLR2A	chr11:85778896-85781451	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAZ	chr11:85777821-85781917	IMR90	lung:	n/a	chr11:85780346-85780365 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85781713-85781722 chr11:85780167-85780176 chr11:85780351-85780360 chr11:85780167-85780176 chr11:85780042-85780052 chr11:85780162-85780181 chr11:85780805-85780816 chr11:85780349-85780362 chr11:85780350-85780361 chr11:85780165-85780178
41	POLR2A	chr11:85777893-85781404	GM12891	blood:	n/a	n/a
42	NFIC	chr11:85780124-85781506	GM12878	blood:	n/a	n/a
43	EP300	chr11:85779123-85781342	GM12878	blood:	n/a	chr11:85780271-85780280 chr11:85781025-85781039 chr11:85779131-85779145 chr11:85781026-85781035
44	POLR2A	chr11:85778740-85781540	IMR90	lung:	n/a	n/a
45	ZNF143	chr11:85780051-85781332	K562	blood:	n/a	chr11:85780270-85780280
46	FOXM1	chr11:85780138-85781353	ECC-1	luminal epithelium:	n/a	n/a
47	SMC3	chr11:85778243-85781361	Hela-S3	cervix:	n/a	chr11:85779975-85779982
48	POLR2A	chr11:85779031-85781323	HUVEC	blood vessel:	n/a	n/a
49	GATA3	chr11:85779901-85781345	SK-N-SH	brain:	n/a	chr11:85781027-85781037
50	TBL1XR1	chr11:85779535-85781367	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85777862..85782517-chr11:85902953..85907117,7	K562	blood:
2	chr11:85775018..85777414-chr11:85781077..85783520,2	K562	blood:
3	chr11:85780488..85782711-chr11:85954373..85957163,3	MCF-7	breast:
4	chr11:85779554..85782905-chr11:85860304..85865248,6	K562	blood:
5	chr11:85778910..85781849-chr11:85954546..85957728,3	K562	blood:
6	chr11:85375979..85377499-chr11:85779750..85781435,2	K562	blood:

Variant related genes	Relation type
PICALM	TF binding region
ENSG00000200877	Chromatin interaction
ENSG00000137504	Chromatin interaction
ENSG00000254699	Chromatin interaction
ENSG00000254502	Chromatin interaction
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11234493	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1237230	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1513390	0.93[ASN][1000 genomes]
rs1996108	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2077815	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2155051	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2458493	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458496	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2458499	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2458500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2508688	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2509608	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2509609	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3016327	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3016786	0.80[CHB][hapmap]
rs472618	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs488134	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs489486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494369	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs497711	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs527162	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs528109	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs536841	0.84[ASW][hapmap];0.89[MKK][hapmap]
rs540422	0.91[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs542167	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs544458	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs544848	0.87[ASN][1000 genomes]
rs547767	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs548121	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs556562	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs583126	0.89[ASN][1000 genomes]
rs585820	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs588076	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs588380	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs592297	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs592314	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs595972	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs597446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs600258	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs600743	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs601185	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs602222	0.82[CHB][hapmap]
rs603615	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs616555	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs618001	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs618629	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs618679	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs622220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs626542	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs627818	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs634719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635168	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs637304	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs645299	0.84[CHB][hapmap]
rs648270	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs654194	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs655641	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs659801	0.88[EUR][1000 genomes]
rs670606	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs676733	0.81[MKK][hapmap]
rs680119	0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs682366	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs682928	0.81[CHB][hapmap]
rs75751	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7938033	0.82[CHB][hapmap]
rs7951988	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867611	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9804630	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs669556	ME3	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85780200-85781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:85780400-85781400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:85780400-85781400	Flanking Active TSS	Fetal Brain Male	brain
4	chr11:85780600-85781400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:85780600-85781400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr11:85780600-85781400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr11:85780600-85781400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:85780600-85781400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr11:85780600-85781400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:85780600-85781400	Flanking Active TSS	Rectal Smooth Muscle	rectum
11	chr11:85780600-85781400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr11:85780600-85781400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr11:85780600-85781400	Flanking Active TSS	GM12878-XiMat	blood
14	chr11:85780600-85781400	Flanking Active TSS	NH-A	brain
15	chr11:85780600-85781600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:85780600-85781600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr11:85780600-85782000	Flanking Active TSS	K562	blood
18	chr11:85780800-85781400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:85780800-85781400	Weak transcription	Aorta	Aorta
20	chr11:85780800-85781400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr11:85780800-85781400	Enhancers	Fetal Stomach	stomach
22	chr11:85780800-85781400	Weak transcription	Left Ventricle	heart
23	chr11:85780800-85781400	Weak transcription	Right Atrium	heart
24	chr11:85780800-85781600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:85780800-85781800	Enhancers	Brain Cingulate Gyrus	brain
26	chr11:85780800-85781800	Enhancers	Fetal Heart	heart
27	chr11:85780800-85782400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr11:85780800-85784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:85781000-85781400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr11:85781000-85781400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:85781000-85781400	Enhancers	Primary B cells from peripheral blood	blood
32	chr11:85781000-85781400	Enhancers	Primary T cells from cord blood	blood
33	chr11:85781000-85781400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr11:85781000-85781400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr11:85781000-85781400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr11:85781000-85781400	Enhancers	Fetal Kidney	kidney
37	chr11:85781000-85781400	Enhancers	Fetal Lung	lung
38	chr11:85781000-85781400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr11:85781000-85781400	Enhancers	Stomach Mucosa	stomach
40	chr11:85781000-85781400	Flanking Active TSS	Hela-S3	cervix
41	chr11:85781000-85781400	Flanking Active TSS	HUVEC	blood vessel
42	chr11:85781000-85781600	Enhancers	Brain Hippocampus Middle	brain
43	chr11:85781000-85781600	Enhancers	Fetal Intestine Small	intestine
44	chr11:85781000-85781600	Flanking Active TSS	HSMM	muscle
45	chr11:85781000-85781800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:85781000-85781800	Enhancers	Colon Smooth Muscle	Colon
47	chr11:85781000-85781800	Enhancers	Fetal Muscle Leg	muscle
48	chr11:85781000-85781800	Enhancers	Fetal Thymus	thymus
49	chr11:85781000-85781800	Enhancers	Thymus	Thymus
50	chr11:85781000-85781800	Enhancers	Spleen	Spleen

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