Variant report

Variant	rs1734908
Chromosome Location	chr7:100313768-100313769
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100311164..100312839-chr7:100313147..100315686,2	MCF-7	breast:
2	chr7:100302051..100306591-chr7:100312993..100321692,11	MCF-7	breast:
3	chr7:100301529..100304641-chr7:100311739..100314929,3	K562	blood:
4	chr7:100313418..100315203-chr7:100315315..100317300,2	K562	blood:

Variant related genes	Relation type
ENSG00000172336	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10277087	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953301	0.89[JPT][hapmap]
rs11520986	0.89[JPT][hapmap]
rs11974395	0.89[JPT][hapmap]
rs11979818	0.89[JPT][hapmap]
rs11983334	0.89[JPT][hapmap]
rs1617640	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	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1734910	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075672	0.86[MEX][hapmap]
rs221771	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221772	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221788	0.85[EUR][1000 genomes]
rs221790	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs221795	0.88[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs221801	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2272572	0.89[JPT][hapmap]
rs2432930	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4727459	0.89[JPT][hapmap]
rs4729597	0.87[MEX][hapmap]
rs4729602	0.89[JPT][hapmap]
rs4729606	0.89[JPT][hapmap]
rs4729607	0.89[JPT][hapmap]
rs475339	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs504141	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs507392	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs551238	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs554055	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs568733	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576236	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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
rs1734908	TAC1	cis	parietal	SCAN
rs1734908	MOSPD3	cis	Whole Blood	GTEx
rs1734908	POLR2J	cis	parietal	SCAN
rs1734908	TSC22D4	cis	parietal	SCAN
rs1734908	PILRB	cis	cerebellum	SCAN
rs1734908	C10orf107	trans	parietal	SCAN
rs1734908	DLX5	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100305000-100318000	Weak transcription	Right Atrium	heart
2	chr7:100305200-100315000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr7:100305200-100318400	Weak transcription	Gastric	stomach
4	chr7:100306200-100314400	Weak transcription	Lung	lung
5	chr7:100306800-100315400	Weak transcription	Placenta	Placenta
6	chr7:100306800-100315600	Weak transcription	HepG2	liver
7	chr7:100312600-100314200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links