Variant report

Variant	rs1617640
Chromosome Location	chr7:100317298-100317299
allele	G/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	HNF4A	chr7:100317298-100317704	HepG2	liver:	n/a	chr7:100317467-100317482
2	HNF4A	chr7:100317265-100317735	HepG2	liver:	n/a	chr7:100317467-100317482
3	FOXA1	chr7:100317191-100317643	HepG2	liver:	n/a	n/a
4	HNF4A	chr7:100317296-100317699	HepG2	liver:	n/a	chr7:100317467-100317482
5	HDAC2	chr7:100317122-100317663	HepG2	liver:	n/a	n/a
6	SMC3	chr7:100317168-100318210	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr7:100317028-100317720	HepG2	liver:	n/a	n/a
8	HNF4G	chr7:100317248-100317689	HepG2	liver:	n/a	chr7:100317437-100317452
9	EP300	chr7:100317135-100317734	HepG2	liver:	n/a	n/a
10	TEAD4	chr7:100317166-100317730	HepG2	liver:	n/a	n/a
11	FOXA2	chr7:100317246-100317708	HepG2	liver:	n/a	n/a
12	NFIC	chr7:100317220-100317618	HepG2	liver:	n/a	n/a
13	SP1	chr7:100317168-100317754	HepG2	liver:	n/a	n/a
14	RCOR1	chr7:100317114-100317380	HepG2	liver:	n/a	n/a
15	HNF4G	chr7:100317267-100317712	HepG2	liver:	n/a	chr7:100317437-100317452
16	CTCF	chr7:100317095-100318171	SK-N-SH	brain:	n/a	chr7:100318063-100318072
17	MYBL2	chr7:100317154-100317778	HepG2	liver:	n/a	n/a
18	RXRA	chr7:100317291-100317805	HepG2	liver:	n/a	n/a
19	FOXA1	chr7:100317133-100317716	HepG2	liver:	n/a	n/a
20	HEY1	chr7:100317196-100317674	HepG2	liver:	n/a	n/a
21	NR2F2	chr7:100317090-100319550	HepG2	liver:	n/a	n/a
22	MAX	chr7:100317046-100319536	HepG2	liver:	n/a	chr7:100318766-100318773 chr7:100318351-100318361
23	FOXA1	chr7:100317250-100317596	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100315279..100318194-chr7:100320126..100322658,3	K562	blood:
2	chr7:100313418..100315203-chr7:100315315..100317300,2	K562	blood:
3	chr7:100315107..100317886-chr7:100488286..100489805,2	MCF-7	breast:
4	chr7:100302553..100308135-chr7:100314195..100322207,16	MCF-7	breast:
5	chr7:100311308..100312814-chr7:100315076..100317499,2	K562	blood:
6	chr7:100302051..100306591-chr7:100312993..100321692,11	MCF-7	breast:
7	chr7:100314177..100318194-chr7:100318771..100321626,3	K562	blood:
8	chr7:100315257..100318069-chr7:100320272..100323098,2	MCF-7	breast:

Variant related genes	Relation type
EPO	TF binding region
ENSG00000172336	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10277087	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1734908	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1734909	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1734910	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2075671	0.90[JPT][hapmap]
rs2075672	0.86[MEX][hapmap]
rs221771	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs221772	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs221788	0.87[EUR][1000 genomes]
rs221790	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs221795	0.84[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap]
rs221801	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.95[EUR][1000 genomes]
rs2293769	0.90[JPT][hapmap]
rs2432930	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4729597	0.87[MEX][hapmap]
rs475339	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs504141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs507392	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs551238	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs554055	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs568733	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs576236	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv888796	chr7:100313420-100423365	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1617640	POLR2J	cis	parietal	SCAN
rs1617640	PILRB	cis	cerebellum	SCAN
rs1617640	DLX5	cis	cerebellum	SCAN
rs1617640	C10orf107	trans	parietal	SCAN
rs1617640	TSC22D4	cis	parietal	SCAN
rs1617640	MOSPD3	cis	Whole Blood	GTEx
rs1617640	TAC1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100305000-100318000	Weak transcription	Right Atrium	heart
2	chr7:100305200-100318400	Weak transcription	Gastric	stomach
3	chr7:100315400-100317400	Enhancers	Placenta	Placenta
4	chr7:100316600-100317800	Weak transcription	Esophagus	oesophagus
5	chr7:100316600-100318400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:100316600-100318400	Enhancers	Liver	Liver
7	chr7:100316800-100318200	Bivalent Enhancer	Fetal Intestine Large	intestine
8	chr7:100317000-100318000	Flanking Active TSS	HepG2	liver
9	chr7:100317200-100317800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:100317200-100317800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
11	chr7:100317200-100319400	Bivalent Enhancer	Fetal Intestine Small	intestine

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