Variant report

Variant	rs12711504
Chromosome Location	chr1:211810171-211810172
allele	C/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	MXI1	chr1:211809581-211810240	Hela-S3	cervix:	n/a	n/a
2	HNF4A	chr1:211809848-211810252	HepG2	liver:	n/a	chr1:211810074-211810096 chr1:211810078-211810092 chr1:211810079-211810092 chr1:211810078-211810091 chr1:211810077-211810092 chr1:211810076-211810094 chr1:211810078-211810093 chr1:211810079-211810092 chr1:211810077-211810092 chr1:211810079-211810091 chr1:211810078-211810092 chr1:211810079-211810092
3	POLR2A	chr1:211809780-211810243	SK-N-SH	brain:	n/a	n/a
4	FOSL2	chr1:211809749-211810286	SK-N-SH	brain:	n/a	n/a
5	SMARCC1	chr1:211809200-211810986	Hela-S3	cervix:	n/a	n/a
6	EP300	chr1:211809812-211810178	SK-N-SH_RA	brain:	n/a	n/a
7	BRCA1	chr1:211809716-211810246	Hela-S3	cervix:	n/a	n/a
8	TEAD4	chr1:211809691-211810223	SK-N-SH	brain:	n/a	n/a
9	GTF2F1	chr1:211809857-211810193	Hela-S3	cervix:	n/a	n/a
10	SP1	chr1:211809728-211810266	A549	lung:	n/a	n/a
11	MAZ	chr1:211809789-211810244	Hela-S3	cervix:	n/a	n/a
12	EP300	chr1:211809627-211810366	SK-N-SH	brain:	n/a	n/a
13	MYC	chr1:211809603-211810256	Hela-S3	cervix:	n/a	n/a
14	JUND	chr1:211809822-211810239	A549	lung:	n/a	n/a
15	SMC3	chr1:211809826-211810227	Hela-S3	cervix:	n/a	n/a
16	GTF3C2	chr1:211808656-211810403	Hela-S3	cervix:	n/a	n/a
17	GATA3	chr1:211809604-211810391	SK-N-SH	brain:	n/a	n/a
18	JUND	chr1:211809806-211810210	Hela-S3	cervix:	n/a	n/a
19	RFX5	chr1:211809782-211810237	Hela-S3	cervix:	n/a	n/a
20	MAX	chr1:211809633-211810297	Hela-S3	cervix:	n/a	n/a
21	MAX	chr1:211809846-211810188	SK-N-SH	brain:	n/a	n/a
22	RPC155	chr1:211809944-211810771	Hela-S3	cervix:	n/a	n/a
23	GATA3	chr1:211809759-211810349	SK-N-SH	brain:	n/a	n/a
24	FOSL2	chr1:211809776-211810190	SK-N-SH	brain:	n/a	n/a
25	TCF12	chr1:211809675-211810247	SK-N-SH	brain:	n/a	n/a
26	RCOR1	chr1:211809558-211810306	Hela-S3	cervix:	n/a	n/a
27	FOSL2	chr1:211809823-211810262	HepG2	liver:	n/a	n/a
28	TEAD4	chr1:211809715-211810202	HepG2	liver:	n/a	n/a
29	HNF4G	chr1:211809850-211810182	HepG2	liver:	n/a	chr1:211810074-211810096 chr1:211810078-211810092 chr1:211810079-211810092 chr1:211810078-211810091 chr1:211810076-211810094 chr1:211810078-211810093 chr1:211810079-211810092 chr1:211810077-211810092 chr1:211810079-211810091 chr1:211810078-211810092 chr1:211810079-211810092
30	SMARCB1	chr1:211809353-211810640	Hela-S3	cervix:	n/a	n/a
31	FOXA1	chr1:211809808-211810215	HepG2	liver:	n/a	n/a
32	MAFK	chr1:211809671-211810223	Hela-S3	cervix:	n/a	n/a
33	RXRA	chr1:211809669-211810385	SK-N-SH	brain:	n/a	chr1:211810079-211810092 chr1:211810078-211810087 chr1:211809967-211809986 chr1:211810079-211810092 chr1:211810077-211810093 chr1:211810079-211810092
34	MYC	chr1:211809862-211810188	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr1:211809839-211810295	Hela-S3	cervix:	n/a	n/a
36	FOXA1	chr1:211809893-211810347	HepG2	liver:	n/a	n/a
37	EP300	chr1:211809825-211810246	HepG2	liver:	n/a	n/a
38	FOS	chr1:211809863-211810177	MCF10A-Er-Src	breast:	n/a	n/a
39	USF2	chr1:211809879-211810201	Hela-S3	cervix:	n/a	n/a
40	EP300	chr1:211809886-211810204	HepG2	liver:	n/a	n/a
41	SP1	chr1:211809699-211810385	HCT-116	colon:	n/a	n/a
42	MAX	chr1:211809838-211810277	HepG2	liver:	n/a	n/a
43	NFIC	chr1:211809723-211810211	SK-N-SH	brain:	n/a	n/a
44	FOXA2	chr1:211809948-211810340	A549	lung:	n/a	n/a
45	TCF12	chr1:211809608-211810395	SK-N-SH	brain:	n/a	n/a
46	FOXA1	chr1:211809897-211810258	HepG2	liver:	n/a	n/a
47	MAX	chr1:211809789-211810191	SK-N-SH	brain:	n/a	n/a
48	RXRA	chr1:211809650-211810402	SK-N-SH	brain:	n/a	chr1:211810079-211810092 chr1:211810078-211810087 chr1:211809967-211809986 chr1:211810079-211810092 chr1:211810077-211810093 chr1:211810079-211810092
49	TCF12	chr1:211809695-211810290	A549	lung:	n/a	n/a
50	SP1	chr1:211809870-211810237	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:211805499..211810389-chr1:211816053..211819078,4	K562	blood:
2	chr1:211808019..211810498-chr1:211819976..211822363,2	K562	blood:
3	chr1:211788189..211791176-chr1:211807791..211810721,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227764	TF binding region
ENSG00000228792	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10157989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158618	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158723	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158740	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577181	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590554	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239534	0.95[ASN][1000 genomes]
rs12711505	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711506	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730869	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749444	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12751564	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755496	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17017855	1.00[ASN][1000 genomes]
rs34028707	0.95[ASN][1000 genomes]
rs4345851	0.81[ASN][1000 genomes]
rs4399227	0.81[ASN][1000 genomes]
rs4562684	0.81[ASN][1000 genomes]
rs4951414	0.85[ASN][1000 genomes]
rs4951417	0.90[ASN][1000 genomes]
rs4951420	0.86[ASN][1000 genomes]
rs6540692	0.81[ASN][1000 genomes]
rs7529914	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765202	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211804200-211813400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:211806800-211811600	Weak transcription	Fetal Intestine Large	intestine
4	chr1:211806800-211813000	Weak transcription	Stomach Mucosa	stomach
5	chr1:211807000-211810600	Weak transcription	Placenta	Placenta
6	chr1:211807000-211811600	Weak transcription	Esophagus	oesophagus
7	chr1:211807000-211812000	Weak transcription	Adipose Nuclei	Adipose
8	chr1:211807000-211816200	Weak transcription	Colonic Mucosa	Colon
9	chr1:211807000-211816200	Weak transcription	Ovary	ovary
10	chr1:211807200-211812000	Weak transcription	NHLF	lung
11	chr1:211807200-211816600	Weak transcription	Right Ventricle	heart
12	chr1:211807200-211817200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:211807400-211812200	Weak transcription	NH-A	brain
14	chr1:211807400-211816800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:211807600-211811600	Weak transcription	Liver	Liver
16	chr1:211807600-211812800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:211807600-211812800	Weak transcription	Pancreas	Pancrea
18	chr1:211807600-211813000	Weak transcription	HSMMtube	muscle
19	chr1:211807600-211816600	Weak transcription	Left Ventricle	heart
20	chr1:211808600-211810800	Enhancers	Osteobl	bone
21	chr1:211808800-211810600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:211809200-211810200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:211809200-211810400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:211809400-211810200	Enhancers	HSMM	muscle
25	chr1:211809400-211810200	Enhancers	NHDF-Ad	bronchial
26	chr1:211809400-211810800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:211809400-211810800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:211809400-211810800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:211809400-211811200	Enhancers	HepG2	liver
30	chr1:211809400-211813000	Enhancers	A549	lung
31	chr1:211809600-211810200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:211809600-211810200	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:211809600-211810200	Enhancers	Fetal Intestine Small	intestine
34	chr1:211809600-211810200	Enhancers	HMEC	breast
35	chr1:211809600-211811000	Enhancers	HUVEC	blood vessel
36	chr1:211809800-211810200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:211809800-211810400	Enhancers	Hela-S3	cervix
38	chr1:211809800-211813000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:211810000-211810600	Enhancers	Spleen	Spleen
40	chr1:211810000-211810800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:211810000-211811600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links