Variant report

Variant	rs7776236
Chromosome Location	chr6:113755212-113755213
allele	C/T
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	CEBPB	chr6:113753887-113755234	Hela-S3	cervix:	n/a	chr6:113754871-113754882 chr6:113754869-113754882
2	ESR1	chr6:113753920-113755353	T-47D	breast:	n/a	n/a
3	ESR1	chr6:113753958-113755288	T-47D	breast:	n/a	n/a
4	ESR1	chr6:113753996-113755245	T-47D	breast:	n/a	n/a
5	FOXA1	chr6:113754019-113755372	T-47D	breast:	n/a	n/a
6	SIN3AK20	chr6:113754259-113755430	MCF-7	breast:	n/a	n/a
7	ESR1	chr6:113753958-113755298	T-47D	breast:	n/a	n/a
8	EP300	chr6:113753838-113755270	A549	lung:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984 chr6:113753873-113753887
9	RAD21	chr6:113754375-113755280	MCF-7	breast:	n/a	n/a
10	GATA3	chr6:113753742-113755812	MCF-7	breast:	n/a	chr6:113753875-113753885 chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
11	CEBPB	chr6:113754484-113755313	MCF-7	breast:	n/a	chr6:113754871-113754882 chr6:113754869-113754882
12	ELF1	chr6:113754531-113755280	MCF-7	breast:	n/a	n/a
13	TEAD4	chr6:113754508-113755372	MCF-7	breast:	n/a	chr6:113755052-113755061
14	GATA3	chr6:113753824-113755522	A549	lung:	n/a	chr6:113753875-113753885 chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
15	FOXA1	chr6:113753961-113755419	T-47D	breast:	n/a	n/a
16	GATA3	chr6:113753876-113755661	MCF-7	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
17	CEBPB	chr6:113753928-113755259	IMR90	lung:	n/a	chr6:113754871-113754882 chr6:113754869-113754882
18	RAD21	chr6:113754704-113755277	IMR90	lung:	n/a	n/a
19	RFX5	chr6:113754180-113755289	Hela-S3	cervix:	n/a	n/a
20	FOXA2	chr6:113753926-113755283	A549	lung:	n/a	n/a
21	NR2F2	chr6:113753989-113755447	MCF-7	breast:	n/a	n/a
22	EP300	chr6:113754103-113755353	T-47D	breast:	n/a	chr6:113755150-113755160
23	EP300	chr6:113753817-113755479	T-47D	breast:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984 chr6:113753873-113753887
24	FOSL2	chr6:113754341-113755361	MCF-7	breast:	n/a	n/a
25	GATA3	chr6:113753950-113755449	T-47D	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
26	CEBPB	chr6:113753852-113755255	A549	lung:	n/a	chr6:113754871-113754882 chr6:113754869-113754882
27	TCF12	chr6:113754049-113755658	MCF-7	breast:	n/a	n/a
28	HDAC2	chr6:113754386-113755290	MCF-7	breast:	n/a	n/a
29	SMC3	chr6:113754160-113755296	Hela-S3	cervix:	n/a	n/a
30	SIN3AK20	chr6:113753876-113755591	MCF-7	breast:	n/a	n/a
31	FOXM1	chr6:113753798-113755513	MCF-7	breast:	n/a	n/a
32	JUND	chr6:113753939-113755483	T-47D	breast:	n/a	chr6:113754145-113754157
33	TFAP2C	chr6:113754555-113755212	Hela-S3	cervix:	n/a	n/a
34	SP1	chr6:113753904-113755294	A549	lung:	n/a	n/a
35	SP1	chr6:113753811-113755252	A549	lung:	n/a	n/a
36	ESR1	chr6:113754373-113755275	T-47D	breast:	n/a	n/a
37	TCF7L2	chr6:113754459-113755295	MCF-7	breast:	n/a	n/a
38	RAD21	chr6:113754454-113755314	MCF-7	breast:	n/a	n/a
39	JUND	chr6:113754276-113755469	T-47D	breast:	n/a	n/a
40	ESR1	chr6:113754380-113755304	T-47D	breast:	n/a	n/a
41	TCF12	chr6:113753707-113755418	A549	lung:	n/a	n/a
42	GATA3	chr6:113753995-113755569	T-47D	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
43	EP300	chr6:113753891-113755256	Hela-S3	cervix:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984
44	GATA3	chr6:113754069-113755578	MCF-7	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
45	ZNF217	chr6:113753995-113755366	MCF-7	breast:	n/a	n/a
46	EP300	chr6:113753973-113755384	MCF-7	breast:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984
47	EP300	chr6:113753838-113755358	A549	lung:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984 chr6:113753873-113753887
48	JUND	chr6:113754289-113755451	MCF-7	breast:	n/a	n/a
49	GATA3	chr6:113754042-113755410	MCF-7	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
50	CEBPB	chr6:113753789-113755513	MCF-7	breast:	n/a	chr6:113754871-113754882 chr6:113754869-113754882

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:113753088..113757268-chr6:113951584..113954499,3	MCF-7	breast:
2	chr6:113753712..113755714-chr6:114178275..114180113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232316	TF binding region
ENSG00000155130	Chromatin interaction
ENSG00000230943	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10080444	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10080706	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1033390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1033391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457266	0.93[EUR][1000 genomes]
rs10484457	0.80[ASN][1000 genomes]
rs10484459	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10872095	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10872097	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153417	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153418	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203134	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214468	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049924	0.82[CHD][hapmap]
rs2092086	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2092087	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2103538	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142641	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2179118	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294231	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2348304	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380793	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4435975	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945948	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5001721	0.87[ASN][1000 genomes]
rs58045871	0.80[ASN][1000 genomes]
rs6568791	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914474	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914499	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938194	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs764733	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs764734	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766329	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766330	0.87[ASN][1000 genomes]
rs7738898	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7758769	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771550	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7771810	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7772108	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7772790	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs909542	0.87[CHD][hapmap]
rs9320453	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320456	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320457	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9320458	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9481352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9481355	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481356	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481357	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481358	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481359	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481360	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481361	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481365	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9488184	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488187	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9488189	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9488190	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9488191	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9488195	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916294	chr6:113518489-113904305	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1034256	chr6:113703567-113793790	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1021815	chr6:113703567-113799956	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1018357	chr6:113748468-113781070	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7776236	RWDD1	cis	cerebellum	SCAN
rs7776236	ZUFSP	cis	parietal	SCAN
rs7776236	RFPL4B	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113753000-113755800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:113753400-113755800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:113753600-113755400	Enhancers	Liver	Liver
4	chr6:113753600-113755400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr6:113753600-113755600	Enhancers	Primary B cells from cord blood	blood
6	chr6:113753600-113755600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:113753600-113755800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:113753600-113755800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:113753600-113755800	Enhancers	NHDF-Ad	bronchial
10	chr6:113753600-113755800	Enhancers	NHLF	lung
11	chr6:113753600-113756200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:113753600-113756600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:113753600-113756800	Enhancers	Osteobl	bone
14	chr6:113753800-113755400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:113753800-113756000	Enhancers	Placenta	Placenta
16	chr6:113753800-113756200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:113753800-113756600	Enhancers	Fetal Lung	lung
18	chr6:113754000-113755800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:113754200-113755600	Enhancers	Adipose Nuclei	Adipose
20	chr6:113754200-113755600	Enhancers	HMEC	breast
21	chr6:113754200-113755800	Enhancers	Fetal Intestine Small	intestine
22	chr6:113754200-113755800	Enhancers	Ovary	ovary
23	chr6:113754200-113756000	Enhancers	Colon Smooth Muscle	Colon
24	chr6:113754200-113756800	Enhancers	Fetal Stomach	stomach
25	chr6:113754400-113755600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:113754400-113755600	Enhancers	Fetal Intestine Large	intestine
27	chr6:113754800-113755400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:113755000-113755400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:113755000-113755600	Flanking Active TSS	A549	lung
30	chr6:113755200-113755800	Enhancers	Hela-S3	cervix
31	chr6:113755200-113756400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr6:113755200-113756800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links