Variant report

Variant	rs2240393
Chromosome Location	chr7:84654731-84654732
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	NFIC	chr7:84654458-84655016	ECC-1	luminal epithelium:	n/a	chr7:84654858-84654874
2	MAX	chr7:84654588-84654994	Hela-S3	cervix:	n/a	n/a
3	EP300	chr7:84654632-84655055	Hela-S3	cervix:	n/a	n/a
4	RFX5	chr7:84654536-84655074	Hela-S3	cervix:	n/a	n/a
5	TCF7L2	chr7:84654644-84654847	PANC-1	pancreas:	n/a	n/a
6	NFIC	chr7:84654588-84655073	ECC-1	luminal epithelium:	n/a	chr7:84654858-84654874
7	EP300	chr7:84654446-84655172	SK-N-SH	brain:	n/a	chr7:84654624-84654638
8	STAT3	chr7:84654587-84655045	Hela-S3	cervix:	n/a	chr7:84655001-84655012 chr7:84654602-84654609
9	ELK1	chr7:84654697-84654979	Hela-S3	cervix:	n/a	n/a
10	EP300	chr7:84654613-84655130	SK-N-SH_RA	brain:	n/a	chr7:84654624-84654638
11	REST	chr7:84654628-84654952	PFSK-1	brain:	n/a	n/a
12	CEBPB	chr7:84654570-84655078	Hela-S3	cervix:	n/a	n/a
13	PRDM1	chr7:84654651-84654982	Hela-S3	cervix:	n/a	n/a
14	MYC	chr7:84654656-84655024	MCF10A-Er-Src	breast:	n/a	n/a
15	NFIC	chr7:84654467-84655198	SK-N-SH	brain:	n/a	chr7:84654858-84654874
16	EP300	chr7:84654595-84655116	SK-N-SH_RA	brain:	n/a	chr7:84654624-84654638
17	PBX3	chr7:84654552-84655165	SK-N-SH	brain:	n/a	n/a
18	GTF2F1	chr7:84654560-84655027	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr7:84654612-84655098	SK-N-SH	brain:	n/a	n/a
20	FOS	chr7:84654586-84655201	MCF10A-Er-Src	breast:	n/a	n/a
21	TCF12	chr7:84654452-84655285	SK-N-SH	brain:	n/a	n/a
22	CHD2	chr7:84654646-84655055	Hela-S3	cervix:	n/a	n/a
23	REST	chr7:84654610-84654970	PFSK-1	brain:	n/a	n/a
24	SIN3AK20	chr7:84654610-84654887	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr7:84654693-84654790	Gliobla	brain:	n/a	n/a
26	NFIC	chr7:84654567-84655117	SK-N-SH	brain:	n/a	chr7:84654858-84654874
27	EP300	chr7:84654580-84655109	ECC-1	luminal epithelium:	n/a	chr7:84654624-84654638
28	FOS	chr7:84654612-84655119	MCF10A-Er-Src	breast:	n/a	n/a
29	SMC3	chr7:84654423-84655047	Hela-S3	cervix:	n/a	n/a
30	TCF7L2	chr7:84654466-84655078	Hela-S3	cervix:	n/a	chr7:84654935-84654942
31	STAT3	chr7:84654269-84655086	MCF10A-Er-Src	breast:	n/a	chr7:84655001-84655012 chr7:84654602-84654609 chr7:84654269-84654280
32	BRCA1	chr7:84654623-84654936	Hela-S3	cervix:	n/a	n/a
33	STAT3	chr7:84654711-84655104	MCF10A-Er-Src	breast:	n/a	chr7:84655001-84655012
34	ZKSCAN1	chr7:84654673-84654935	Hela-S3	cervix:	n/a	n/a
35	PBX3	chr7:84654585-84655261	SK-N-SH	brain:	n/a	n/a
36	GATA3	chr7:84654452-84655267	SK-N-SH	brain:	n/a	chr7:84655102-84655114
37	TCF12	chr7:84654488-84655226	SK-N-SH	brain:	n/a	n/a
38	TAF1	chr7:84654616-84655080	PFSK-1	brain:	n/a	n/a
39	RCOR1	chr7:84654562-84654992	Hela-S3	cervix:	n/a	n/a
40	TFAP2C	chr7:84654463-84655169	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr7:84654631-84654941	MCF10A-Er-Src	breast:	n/a	n/a
42	TFAP2A	chr7:84654437-84655194	Hela-S3	cervix:	n/a	n/a
43	MYC	chr7:84654665-84655003	MCF10A-Er-Src	breast:	n/a	n/a
44	RAD21	chr7:84654666-84654999	Hela-S3	cervix:	n/a	chr7:84654898-84654912
45	GATA3	chr7:84654468-84655189	SK-N-SH	brain:	n/a	chr7:84655102-84655114

Variant related genes	Relation type
HSPA8P16	TF binding region

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1016027	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10225455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10231441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10237102	0.96[EUR][1000 genomes]
rs10244898	0.93[EUR][1000 genomes]
rs10247311	0.87[EUR][1000 genomes]
rs10256889	0.91[EUR][1000 genomes]
rs10260131	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10261725	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs10264465	0.88[EUR][1000 genomes]
rs10267189	0.91[EUR][1000 genomes]
rs10268216	0.93[EUR][1000 genomes]
rs10271823	0.93[EUR][1000 genomes]
rs10277834	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10281252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10282482	0.89[EUR][1000 genomes]
rs10486845	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10486847	0.85[CEU][hapmap]
rs11760335	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11766179	0.90[EUR][1000 genomes]
rs11771699	0.88[EUR][1000 genomes]
rs11980498	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980984	0.96[EUR][1000 genomes]
rs11982720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12112643	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12113270	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12154971	0.96[EUR][1000 genomes]
rs12155292	0.96[EUR][1000 genomes]
rs12707691	0.95[EUR][1000 genomes]
rs12707692	0.95[EUR][1000 genomes]
rs12707693	0.93[EUR][1000 genomes]
rs12707695	0.95[EUR][1000 genomes]
rs12707696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230423	0.92[EUR][1000 genomes]
rs13231019	0.95[EUR][1000 genomes]
rs13231340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13232515	0.93[EUR][1000 genomes]
rs13232613	0.93[EUR][1000 genomes]
rs13232789	0.91[EUR][1000 genomes]
rs13233871	0.95[EUR][1000 genomes]
rs13234489	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13234914	0.95[EUR][1000 genomes]
rs13240751	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13242253	0.87[EUR][1000 genomes]
rs13244179	0.93[EUR][1000 genomes]
rs13307855	0.94[EUR][1000 genomes]
rs1468396	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1528621	0.93[EUR][1000 genomes]
rs1534565	0.83[EUR][1000 genomes]
rs1534566	0.87[EUR][1000 genomes]
rs1534572	0.90[EUR][1000 genomes]
rs17159470	0.91[EUR][1000 genomes]
rs17558957	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17559084	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17559978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17639510	0.96[EUR][1000 genomes]
rs17639600	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1919282	0.95[EUR][1000 genomes]
rs2040954	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040957	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2103312	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2141415	0.93[EUR][1000 genomes]
rs2158727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178236	0.93[EUR][1000 genomes]
rs2190211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2190213	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2214820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286189	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2372503	0.92[EUR][1000 genomes]
rs2372510	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2372511	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28819164	0.92[EUR][1000 genomes]
rs34004921	0.95[EUR][1000 genomes]
rs34134012	0.94[EUR][1000 genomes]
rs34462522	0.93[EUR][1000 genomes]
rs34584772	0.93[EUR][1000 genomes]
rs34931062	0.96[EUR][1000 genomes]
rs34996468	0.95[EUR][1000 genomes]
rs35003658	0.96[EUR][1000 genomes]
rs35367762	0.87[EUR][1000 genomes]
rs35449238	0.93[EUR][1000 genomes]
rs35600623	0.95[EUR][1000 genomes]
rs35826544	0.95[EUR][1000 genomes]
rs35853835	0.95[EUR][1000 genomes]
rs35948002	0.86[EUR][1000 genomes]
rs36201011	0.82[EUR][1000 genomes]
rs4141132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560742	0.93[EUR][1000 genomes]
rs56039102	0.96[EUR][1000 genomes]
rs56227953	0.86[EUR][1000 genomes]
rs57531424	0.96[EUR][1000 genomes]
rs59006756	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62472060	0.89[EUR][1000 genomes]
rs62472062	0.89[EUR][1000 genomes]
rs62472078	0.92[EUR][1000 genomes]
rs62472081	0.91[EUR][1000 genomes]
rs62472087	0.93[EUR][1000 genomes]
rs62472088	0.93[EUR][1000 genomes]
rs62472110	0.96[EUR][1000 genomes]
rs62472151	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6468010	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6959903	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6962714	0.94[EUR][1000 genomes]
rs6965396	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs713153	0.93[EUR][1000 genomes]
rs713154	0.95[EUR][1000 genomes]
rs71560707	0.93[EUR][1000 genomes]
rs7776699	0.93[EUR][1000 genomes]
rs7777682	0.93[EUR][1000 genomes]
rs7780675	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7788896	0.95[EUR][1000 genomes]
rs7790637	0.93[EUR][1000 genomes]
rs7790809	0.93[EUR][1000 genomes]
rs7793649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7794144	0.93[EUR][1000 genomes]
rs7794619	0.93[EUR][1000 genomes]
rs7794920	0.95[EUR][1000 genomes]
rs7798487	0.91[EUR][1000 genomes]
rs7800072	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7801626	0.92[EUR][1000 genomes]
rs7803548	0.95[EUR][1000 genomes]
rs7806400	0.96[CEU][hapmap]
rs7807283	0.93[EUR][1000 genomes]
rs7809383	0.95[EUR][1000 genomes]
rs9642196	0.93[EUR][1000 genomes]
rs9942642	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949446	chr7:84003501-84763823	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2422324	chr7:84530290-84944913	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:84644600-84662600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:84649600-84654800	Weak transcription	Fetal Lung	lung
3	chr7:84649800-84654800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:84654000-84655400	Enhancers	Fetal Heart	heart
5	chr7:84654000-84655600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:84654000-84655600	Enhancers	HUVEC	blood vessel
7	chr7:84654200-84655400	Enhancers	NHEK	skin
8	chr7:84654400-84655600	Enhancers	GM12878-XiMat	blood
9	chr7:84654600-84654800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:84654600-84655000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:84654600-84655000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:84654600-84655000	Enhancers	Aorta	Aorta
13	chr7:84654600-84655000	Enhancers	Fetal Brain Male	brain
14	chr7:84654600-84655000	Flanking Active TSS	Hela-S3	cervix
15	chr7:84654600-84655200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:84654600-84655200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr7:84654600-84655400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr7:84654600-84655400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:84654600-84655400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr7:84654600-84655600	Enhancers	HMEC	breast
21	chr7:84654600-84655800	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links