Variant report

Variant	rs7608175
Chromosome Location	chr2:234599089-234599090
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr2:234599043-234599396	A549	lung:	n/a	n/a
2	STAT3	chr2:234598953-234599555	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr2:234598994-234599566	MCF-7	breast:	n/a	n/a
4	GATA3	chr2:234598889-234599641	MCF-7	breast:	n/a	chr2:234599154-234599162
5	STAT3	chr2:234598986-234599544	Hela-S3	cervix:	n/a	n/a
6	SP1	chr2:234598804-234599621	A549	lung:	n/a	n/a
7	TFAP2C	chr2:234599025-234599514	Hela-S3	cervix:	n/a	n/a
8	FOS	chr2:234599033-234599557	MCF10A-Er-Src	breast:	n/a	n/a
9	GATA3	chr2:234598953-234599780	MCF-7	breast:	n/a	chr2:234599154-234599162
10	CEBPB	chr2:234598983-234599443	MCF-7	breast:	n/a	n/a
11	JUND	chr2:234599053-234599457	Hela-S3	cervix:	n/a	n/a
12	HDAC2	chr2:234598942-234599469	MCF-7	breast:	n/a	n/a
13	NR2F2	chr2:234598923-234599600	MCF-7	breast:	n/a	n/a
14	FOS	chr2:234599035-234599524	Hela-S3	cervix:	n/a	n/a
15	RFX5	chr2:234599023-234599487	Hela-S3	cervix:	n/a	n/a
16	FOS	chr2:234599066-234599451	MCF10A-Er-Src	breast:	n/a	n/a
17	TCF7L2	chr2:234599061-234599488	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr2:234599009-234599489	Hela-S3	cervix:	n/a	n/a
19	STAT3	chr2:234599077-234599446	MCF10A-Er-Src	breast:	n/a	n/a
20	MYC	chr2:234599073-234599569	MCF10A-Er-Src	breast:	n/a	n/a
21	FOSL2	chr2:234598933-234599481	MCF-7	breast:	n/a	n/a
22	EP300	chr2:234598875-234599622	A549	lung:	n/a	n/a
23	SIN3AK20	chr2:234598818-234599628	MCF-7	breast:	n/a	n/a
24	FOSL2	chr2:234599051-234599456	MCF-7	breast:	n/a	n/a
25	CEBPB	chr2:234599021-234599474	Hela-S3	cervix:	n/a	n/a
26	TFAP2A	chr2:234598925-234599453	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr2:234598794-234599850	A549	lung:	n/a	n/a
28	EP300	chr2:234599017-234599559	Hela-S3	cervix:	n/a	n/a
29	ZNF217	chr2:234599049-234599489	MCF-7	breast:	n/a	n/a
30	MYC	chr2:234598975-234599649	MCF10A-Er-Src	breast:	n/a	n/a
31	TBP	chr2:234599051-234599632	Hela-S3	cervix:	n/a	n/a
32	SMC3	chr2:234599055-234599632	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:234599001-234599491	MCF10A-Er-Src	breast:	n/a	n/a
34	GATA3	chr2:234599004-234599413	T-47D	breast:	n/a	chr2:234599154-234599162
35	EP300	chr2:234598939-234599517	A549	lung:	n/a	n/a
36	FOS	chr2:234599023-234599557	MCF10A-Er-Src	breast:	n/a	n/a
37	GATA3	chr2:234598865-234599680	MCF-7	breast:	n/a	chr2:234599154-234599162
38	RCOR1	chr2:234599049-234599478	Hela-S3	cervix:	n/a	n/a
39	STAT3	chr2:234599029-234599565	MCF10A-Er-Src	breast:	n/a	n/a
40	GATA3	chr2:234599032-234599435	SK-N-SH	brain:	n/a	chr2:234599154-234599162
41	FOS	chr2:234599035-234599543	MCF10A-Er-Src	breast:	n/a	n/a
42	HDAC2	chr2:234598997-234599405	MCF-7	breast:	n/a	n/a
43	FOSL2	chr2:234598827-234599841	A549	lung:	n/a	n/a
44	GATA3	chr2:234598791-234599803	A549	lung:	n/a	chr2:234599154-234599162
45	GATA3	chr2:234598999-234599503	SK-N-SH	brain:	n/a	chr2:234599154-234599162
46	CHD2	chr2:234599081-234599454	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234356284..234357802-chr2:234598772..234601558,2	MCF-7	breast:
2	chr2:234473282..234477495-chr2:234598048..234603332,9	MCF-7	breast:
3	chr2:234385869..234388276-chr2:234598352..234599952,2	MCF-7	breast:
4	chr2:234464216..234467169-chr2:234597494..234599447,2	MCF-7	breast:
5	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
6	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:
7	chr2:234472037..234477650-chr2:234599067..234602356,8	MCF-7	breast:
8	chr2:234578802..234581575-chr2:234598668..234600515,2	MCF-7	breast:
9	chr2:234597435..234606028-chr2:234613419..234620116,22	MCF-7	breast:
10	chr15:50714595..50716933-chr2:234599004..234601578,2	MCF-7	breast:

No data

Variant related genes	Relation type
UGT1A6	TF binding region
ENSG00000085982	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000241119	Chromatin interaction
ENSG00000241635	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000224814	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10167119	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10168155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10171367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10175809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179094	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10189426	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10197460	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10202865	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10203266	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10445704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105879	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105880	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692021	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11692664	0.92[ASN][1000 genomes]
rs11902131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615708	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12623271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13015720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875263	0.83[GIH][hapmap]
rs1983023	0.80[CEU][hapmap]
rs2018985	0.81[CEU][hapmap]
rs2070959	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35984508	0.90[ASN][1000 genomes]
rs3806598	0.81[ASN][1000 genomes]
rs4261716	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4338954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4347832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530361	0.83[CEU][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4553819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45615240	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6725478	0.81[CEU][hapmap]
rs6736508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736743	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349250	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7563561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7577677	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7583278	0.81[CEU][hapmap]
rs7586110	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7592281	0.82[ASN][1000 genomes]
rs869283	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
5	nsv876016	chr2:234590527-234601669	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7608175	ITM2C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234590800-234599800	Weak transcription	Esophagus	oesophagus
2	chr2:234596800-234600600	Enhancers	Stomach Mucosa	stomach
3	chr2:234597000-234600400	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr2:234597400-234599400	Enhancers	HUVEC	blood vessel
5	chr2:234597400-234600800	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr2:234597400-234601000	Enhancers	Hela-S3	cervix
7	chr2:234597600-234600600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:234597800-234608600	Weak transcription	Gastric	stomach
9	chr2:234598000-234599800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:234598000-234600000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:234598200-234599200	Enhancers	NHEK	skin
12	chr2:234598200-234600400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:234598200-234600400	Enhancers	HMEC	breast
14	chr2:234598200-234600600	Weak transcription	Liver	Liver
15	chr2:234598400-234599600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:234598400-234599600	Weak transcription	Colonic Mucosa	Colon
17	chr2:234598400-234600200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:234598400-234600200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:234598800-234600600	Enhancers	Duodenum Mucosa	Duodenum
20	chr2:234599000-234599400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:234599000-234599600	Flanking Active TSS	A549	lung

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