Variant report

Variant	rs661254
Chromosome Location	chr6:128039966-128039967
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	chr6:128039677..128041360-chr6:128042682..128045545,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10457503	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12206811	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1448051	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17054975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs270010	0.82[MEX][hapmap]
rs2786230	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3009959	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35182011	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs471565	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476132	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs476366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs494043	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs495063	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs498692	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs513605	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs513716	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs525267	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs525850	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs527206	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs528725	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs540252	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs540328	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs543982	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs546732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553910	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs557258	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs559832	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs566051	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs568675	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs570462	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57595174	0.94[ASN][1000 genomes]
rs579177	0.80[TSI][hapmap]
rs579512	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs580388	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs586500	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs601132	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs613936	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs620250	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs629648	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs641326	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs643912	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs658838	0.96[ASN][1000 genomes]
rs668527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs675531	0.81[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs677431	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680461	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6918575	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6934865	0.81[AMR][1000 genomes]
rs722916	0.94[ASN][1000 genomes]
rs72968949	0.85[ASN][1000 genomes]
rs7776202	0.81[AMR][1000 genomes]
rs9482835	0.89[MEX][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886638	chr6:127954614-128087172	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv886639	chr6:127954614-128109244	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv886640	chr6:127961263-128096587	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886641	chr6:127971136-128085283	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv886642	chr6:127971136-128096587	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv886643	chr6:127971136-128109244	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv886644	chr6:127976408-128109244	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv886645	chr6:127977160-128085283	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv886646	chr6:127977160-128087172	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv886647	chr6:127977160-128109244	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv886648	chr6:127983009-128109244	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv830799	chr6:128033100-128194511	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128024400-128041200	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr6:128024600-128051400	Strong transcription	Fetal Thymus	thymus
3	chr6:128024800-128041000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:128024800-128042400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:128025200-128047400	Strong transcription	Primary T cells from cord blood	blood
6	chr6:128026400-128049200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:128034600-128041200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:128035000-128040000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:128036400-128040400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:128037400-128041000	Enhancers	Fetal Heart	heart
11	chr6:128037400-128041200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:128038000-128040000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:128038200-128043200	Weak transcription	Ovary	ovary
14	chr6:128038600-128040000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:128038800-128043800	Weak transcription	Thymus	Thymus
16	chr6:128039400-128041000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:128039800-128041000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:128039800-128045400	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:128039800-128046000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:128039800-128069200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links