Variant report

Variant	rs10948271
Chromosome Location	chr6:45978143-45978144
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	chr6:45965967..45967545-chr6:45976025..45978546,2	K562	blood:
2	chr6:45972108..45974934-chr6:45976922..45979622,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10456555	0.84[CHB][hapmap];0.87[ASN][1000 genomes]
rs10456556	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs10456557	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs10807331	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10948268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10948269	0.94[ASN][1000 genomes]
rs10948272	1.00[ASW][hapmap];0.87[CHB][hapmap]
rs12197310	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12197333	0.95[ASN][1000 genomes]
rs12206357	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1338467	1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs1338469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1338472	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1338473	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1338474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1416168	0.87[ASN][1000 genomes]
rs1416169	0.87[ASN][1000 genomes]
rs1535109	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1555216	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1555218	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2021683	0.87[ASN][1000 genomes]
rs2021684	0.87[ASN][1000 genomes]
rs2021687	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2039716	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2144162	0.87[ASN][1000 genomes]
rs2144163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34495744	0.87[ASN][1000 genomes]
rs35293483	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3777605	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3777606	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3777611	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3777613	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3777616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3777619	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3777620	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3777621	0.99[ASN][1000 genomes]
rs3777623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777629	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56968247	0.87[ASN][1000 genomes]
rs57300420	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59981678	0.87[ASN][1000 genomes]
rs6458484	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67921622	0.83[ASN][1000 genomes]
rs6930840	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7764538	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs7771614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7771749	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9689318	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9689699	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9689703	0.82[AMR][1000 genomes];0.98[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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv428482	chr6:45926644-46050182	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv885867	chr6:45936223-45982976	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1025846	chr6:45955173-46047269	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45966200-45978200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:45968000-45979400	Enhancers	Right Ventricle	heart
3	chr6:45969200-45978400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr6:45969400-45978800	Weak transcription	Spleen	Spleen
5	chr6:45970600-45978200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:45973200-45981600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:45976000-45981400	Enhancers	Psoas Muscle	Psoas
8	chr6:45977200-45978400	Enhancers	Hela-S3	cervix
9	chr6:45977400-45978200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:45977400-45979000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr6:45977400-45979000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:45977400-45979000	Enhancers	Right Atrium	heart
13	chr6:45977400-45979200	Enhancers	Lung	lung
14	chr6:45977400-45980200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:45977600-45978400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:45977600-45978400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:45977600-45979000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:45977600-45979000	Weak transcription	Fetal Heart	heart
19	chr6:45977600-45979200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr6:45977800-45978800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:45977800-45979000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:45977800-45980000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:45978000-45978400	Genic enhancers	Fetal Intestine Large	intestine
24	chr6:45978000-45978600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:45978000-45978600	Genic enhancers	Fetal Intestine Small	intestine
26	chr6:45978000-45978800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr6:45978000-45978800	Enhancers	GM12878-XiMat	blood
28	chr6:45978000-45979000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:45978000-45979000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:45978000-45979000	Enhancers	Left Ventricle	heart
31	chr6:45978000-45979800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr6:45978000-45980800	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links