Variant report

Variant	rs17680708
Chromosome Location	chr7:66440252-66440253
allele	A/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	USF1	chr7:66440154-66440511	H1-hESC	embryonic stem cell:	n/a	chr7:66440358-66440369
2	USF1	chr7:66440146-66440477	K562	blood:	n/a	chr7:66440358-66440369
3	JUND	chr7:66440178-66440517	K562	blood:	n/a	chr7:66440330-66440341
4	CHD2	chr7:66440246-66440498	K562	blood:	n/a	n/a
5	ATF3	chr7:66440226-66440478	K562	blood:	n/a	n/a
6	USF1	chr7:66440226-66440536	SK-N-SH	brain:	n/a	chr7:66440358-66440369
7	FOS	chr7:66440240-66440549	K562	blood:	n/a	n/a
8	USF1	chr7:66440188-66440485	A549	lung:	n/a	chr7:66440358-66440369
9	USF1	chr7:66440204-66440515	K562	blood:	n/a	chr7:66440358-66440369
10	POLR2A	chr7:66440248-66440270	K562	blood:	n/a	n/a
11	USF1	chr7:66440185-66440543	ECC-1	luminal epithelium:	n/a	chr7:66440358-66440369
12	USF1	chr7:66440181-66440576	ECC-1	luminal epithelium:	n/a	chr7:66440358-66440369
13	NFYB	chr7:66440213-66440600	K562	blood:	n/a	chr7:66440343-66440358
14	USF1	chr7:66440169-66440560	A549	lung:	n/a	chr7:66440358-66440369
15	EP300	chr7:66440197-66440489	GM12878	blood:	n/a	n/a
16	NFYA	chr7:66440240-66440593	K562	blood:	n/a	chr7:66440417-66440435
17	USF2	chr7:66440246-66440518	K562	blood:	n/a	n/a
18	USF2	chr7:66440210-66440532	H1-hESC	embryonic stem cell:	n/a	n/a
19	SP1	chr7:66440114-66440489	H1-hESC	embryonic stem cell:	n/a	n/a
20	SP1	chr7:66440197-66440548	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr7:66440129-66440356	K562	blood:	n/a	n/a
22	TBP	chr7:66440134-66440682	K562	blood:	n/a	n/a
23	POLR2A	chr7:66440105-66440327	K562	blood:	n/a	n/a
24	POLR2A	chr7:66440090-66440431	K562	blood:	n/a	n/a
25	USF1	chr7:66440200-66440493	A549	lung:	n/a	chr7:66440358-66440369
26	CHD2	chr7:66440195-66440484	H1-hESC	embryonic stem cell:	n/a	n/a
27	HEY1	chr7:66440082-66440383	K562	blood:	n/a	n/a
28	CBX3	chr7:66440088-66440402	K562	blood:	n/a	n/a
29	USF1	chr7:66440180-66440591	H1-hESC	embryonic stem cell:	n/a	chr7:66440358-66440369
30	IRF1	chr7:66440206-66440596	K562	blood:	n/a	n/a
31	POLR2A	chr7:66440208-66440269	K562	blood:	n/a	n/a
32	TBP	chr7:66440149-66440507	H1-hESC	embryonic stem cell:	n/a	n/a
33	EP300	chr7:66440178-66440664	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66430596..66433000-chr7:66437729..66440706,2	K562	blood:
2	chr7:66439219..66440739-chr8:101726060..101728497,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SBDS-1	chr7:66440229-66440267	XLOC_006483
2	lnc-SBDS-1	chr7:66440233-66440267	XLOC_006483

Variant related genes	Relation type
RN7SL43P	TF binding region
ENSG00000070756	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10156059	0.80[ASN][1000 genomes]
rs10228964	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10231411	0.90[TSI][hapmap]
rs10264433	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10264555	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10266792	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10280816	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1060527	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1064795	0.86[TSI][hapmap]
rs13437994	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17748115	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17748222	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28472679	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28501161	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28641990	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28675035	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28817095	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3800818	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59693594	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6965680	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6971508	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71526586	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73143921	0.80[ASN][1000 genomes]
rs73145924	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73151646	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73151663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73151665	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7777631	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs7785883	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7809359	0.82[ASN][1000 genomes]
rs7809535	0.82[ASN][1000 genomes]
rs868960	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv966836	chr7:66438146-66457576	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17680708	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs17680708	CRCP	cis	cerebellum	SCAN
rs17680708	GUSB	cis	cerebellum	SCAN
rs17680708	CRCP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66420600-66459200	Weak transcription	Psoas Muscle	Psoas
2	chr7:66426400-66453200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:66427000-66444800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:66433200-66458600	Weak transcription	Right Atrium	heart
5	chr7:66438800-66444800	Weak transcription	Fetal Intestine Small	intestine
6	chr7:66439000-66445000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:66439600-66441200	Enhancers	K562	blood
8	chr7:66440000-66440400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:66440200-66440400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr7:66440200-66440600	Enhancers	Dnd41	blood

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