Variant report

Variant	rs6460942
Chromosome Location	chr7:12420989-12420990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:173623488..173624406-chr7:12420850..12421512,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10225369	0.87[YRI][hapmap]
rs10229433	0.81[EUR][1000 genomes]
rs10236122	1.00[YRI][hapmap]
rs10267801	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273045	1.00[ASN][1000 genomes]
rs10276171	1.00[ASN][1000 genomes]
rs10488158	1.00[ASN][1000 genomes]
rs12699381	1.00[ASN][1000 genomes]
rs12699388	1.00[ASN][1000 genomes]
rs12699391	1.00[ASN][1000 genomes]
rs12699392	1.00[ASN][1000 genomes]
rs13221702	1.00[ASN][1000 genomes]
rs13235488	1.00[ASN][1000 genomes]
rs13245635	1.00[ASN][1000 genomes]
rs13247370	1.00[ASN][1000 genomes]
rs1595800	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595802	0.80[CEU][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191008	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17274870	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277369	1.00[ASN][1000 genomes]
rs17443848	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs17444044	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444141	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17448913	1.00[ASN][1000 genomes]
rs17541242	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17544637	1.00[ASN][1000 genomes]
rs17670901	0.81[AMR][1000 genomes]
rs17671056	0.81[AMR][1000 genomes]
rs1866650	1.00[ASN][1000 genomes]
rs2033871	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053378	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053381	0.90[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053382	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28366613	1.00[ASN][1000 genomes]
rs34644264	1.00[ASN][1000 genomes]
rs34868445	1.00[ASN][1000 genomes]
rs34915661	1.00[ASN][1000 genomes]
rs35589221	1.00[ASN][1000 genomes]
rs3887296	0.89[CEU][hapmap]
rs4719315	1.00[ASN][1000 genomes]
rs4721088	0.81[AMR][1000 genomes]
rs4721105	1.00[ASN][1000 genomes]
rs4721106	1.00[ASN][1000 genomes]
rs4721107	1.00[ASN][1000 genomes]
rs4721108	1.00[ASN][1000 genomes]
rs62447638	1.00[ASN][1000 genomes]
rs62447639	1.00[ASN][1000 genomes]
rs62447640	1.00[ASN][1000 genomes]
rs62447641	1.00[ASN][1000 genomes]
rs62447642	1.00[ASN][1000 genomes]
rs62448562	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448563	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448565	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62448566	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448568	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448593	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448594	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448596	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448597	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448600	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448602	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448619	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448620	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448621	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448623	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62449509	1.00[ASN][1000 genomes]
rs62451461	0.81[AMR][1000 genomes]
rs62451486	0.81[AMR][1000 genomes]
rs6460935	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460936	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460938	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944134	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944517	1.00[ASN][1000 genomes]
rs6945067	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948314	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948654	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961238	1.00[ASN][1000 genomes]
rs6966791	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968277	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs6968664	1.00[ASN][1000 genomes]
rs6968695	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969309	1.00[ASN][1000 genomes]
rs6970095	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977059	1.00[ASN][1000 genomes]
rs7791634	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796485	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802454	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808537	1.00[ASN][1000 genomes]
rs7808819	0.80[AMR][1000 genomes]
rs7809263	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811374	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv1029941	chr7:12351595-12444490	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv433030	chr7:12352210-12443042	Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1034475	chr7:12352210-12444490	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1029098	chr7:12354108-12443042	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv887631	chr7:12360805-12434771	Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv887632	chr7:12360805-12439672	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv464371	chr7:12371801-12434771	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv606223	chr7:12371801-12434771	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv887633	chr7:12371801-12439672	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv2763622	chr7:12375528-12424583	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv887634	chr7:12385391-12439672	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv470044	chr7:12392897-12434771	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv464373	chr7:12406826-12536336	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv606224	chr7:12406826-12536336	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv887635	chr7:12410112-12474635	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
20	nsv464374	chr7:12414725-12430615	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv606225	chr7:12414725-12430615	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6460942	THSD7A	cis	parietal	SCAN
rs6460942	TMEM106B	Cis_1M	lymphoblastoid	RTeQTL
rs6460942	VWDE	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12368200-12433200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:12381800-12429000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:12403200-12422200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:12418600-12423200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:12418800-12422200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:12418800-12428600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:12418800-12428600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:12419200-12422800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:12419200-12423400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:12419200-12432800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:12420200-12422600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:12420400-12423200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:12420400-12423800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:12420400-12424000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:12420400-12428200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:12420400-12437600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:12420600-12422000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:12420600-12422400	Weak transcription	K562	blood
19	chr7:12420600-12422600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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