Variant report

Variant	rs225678
Chromosome Location	chr6:142517609-142517610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11758623	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs178783	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225601	0.91[ASN][1000 genomes]
rs225602	0.91[ASN][1000 genomes]
rs225604	1.00[JPT][hapmap]
rs225605	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs225606	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs225618	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs225620	1.00[JPT][hapmap]
rs225622	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225623	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs225624	1.00[JPT][hapmap]
rs225629	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs225630	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225631	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs225632	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225633	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225634	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs225635	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225636	0.93[ASN][1000 genomes]
rs225639	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs225640	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225641	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225642	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225643	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225650	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225651	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225652	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225653	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225654	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225655	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225656	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs225657	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs225658	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs225659	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs225660	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225661	0.87[ASN][1000 genomes]
rs225662	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225663	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs225664	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225665	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225666	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225667	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225668	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225670	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225671	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225672	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225673	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225674	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225675	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225676	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225679	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225680	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225682	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225683	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225684	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225685	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225687	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225688	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs225689	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225690	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225692	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225693	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225695	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225696	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225697	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225698	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225700	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225701	1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225702	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225704	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225705	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225706	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225707	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225708	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225709	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225710	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225728	0.83[ASN][1000 genomes]
rs4896574	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4896575	0.90[JPT][hapmap]
rs56185739	0.95[ASN][1000 genomes]
rs62430473	0.91[ASN][1000 genomes]
rs62430506	0.85[ASN][1000 genomes]
rs628311	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs638804	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639658	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9321861	0.90[JPT][hapmap]
rs9389979	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9389980	0.81[CHB][hapmap];0.90[JPT][hapmap]

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	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142484200-142533800	Weak transcription	Aorta	Aorta
2	chr6:142489000-142543200	Weak transcription	Small Intestine	intestine
3	chr6:142492200-142524800	Weak transcription	Brain Angular Gyrus	brain
4	chr6:142495600-142533600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:142495800-142519600	Weak transcription	HMEC	breast
6	chr6:142496000-142525000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:142496000-142528600	Weak transcription	Lung	lung
8	chr6:142496200-142519400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:142496200-142519600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:142496200-142527600	Weak transcription	Thymus	Thymus
11	chr6:142496200-142528200	Weak transcription	Fetal Stomach	stomach
12	chr6:142496200-142528400	Weak transcription	Brain Germinal Matrix	brain
13	chr6:142496200-142533800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:142496200-142533800	Weak transcription	Gastric	stomach
15	chr6:142496200-142533800	Weak transcription	Pancreas	Pancrea
16	chr6:142496400-142528000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:142496400-142533600	Weak transcription	Colonic Mucosa	Colon
18	chr6:142496600-142519600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:142496600-142525800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:142496600-142526200	Weak transcription	Esophagus	oesophagus
21	chr6:142496600-142533800	Weak transcription	Left Ventricle	heart
22	chr6:142496600-142546800	Weak transcription	NHLF	lung
23	chr6:142498200-142526000	Weak transcription	Fetal Intestine Small	intestine
24	chr6:142498600-142519600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:142498600-142527800	Weak transcription	Ovary	ovary
26	chr6:142499200-142524800	Weak transcription	HSMMtube	muscle
27	chr6:142499400-142519600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:142499600-142519600	Weak transcription	Brain Anterior Caudate	brain
29	chr6:142499600-142519600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:142499600-142519600	Weak transcription	Fetal Brain Female	brain
31	chr6:142499600-142521000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:142499600-142521200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:142500000-142519600	Weak transcription	Fetal Kidney	kidney
34	chr6:142500200-142519600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:142500600-142519400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:142501400-142522400	Weak transcription	K562	blood
37	chr6:142502000-142527800	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:142504200-142519400	Weak transcription	GM12878-XiMat	blood
39	chr6:142504400-142519600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:142507800-142533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:142508200-142525000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:142508600-142519600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:142509200-142526000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:142510400-142534000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:142510400-142534200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:142510600-142519600	Weak transcription	Fetal Intestine Large	intestine
47	chr6:142510600-142519600	Weak transcription	Fetal Lung	lung
48	chr6:142510800-142534600	Weak transcription	Hela-S3	cervix
49	chr6:142511600-142519400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:142511600-142519600	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