Variant report

Variant	rs225659
Chromosome Location	chr6:142488115-142488116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11758623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs178783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225601	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225602	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225604	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs225605	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs225606	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225618	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225620	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs225622	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225623	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225624	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225628	0.91[EUR][1000 genomes]
rs225629	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225630	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225631	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225632	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225633	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225634	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225635	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225636	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225637	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs225639	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225640	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225641	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225642	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225643	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225650	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225651	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225655	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225656	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs225657	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs225658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225661	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225664	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225666	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225667	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225668	0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225670	0.99[ASN][1000 genomes]
rs225671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs225672	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs225677	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs225678	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs225679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225680	0.96[ASN][1000 genomes]
rs225682	0.96[ASN][1000 genomes]
rs225683	0.96[ASN][1000 genomes]
rs225684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225686	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs225687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225688	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs225689	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs225690	0.96[ASN][1000 genomes]
rs225692	0.96[ASN][1000 genomes]
rs225693	0.96[ASN][1000 genomes]
rs225695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225696	0.96[ASN][1000 genomes]
rs225697	0.96[ASN][1000 genomes]
rs225698	0.96[ASN][1000 genomes]
rs225700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225701	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs225704	0.96[ASN][1000 genomes]
rs225705	0.96[ASN][1000 genomes]
rs225706	0.96[ASN][1000 genomes]
rs225707	0.96[ASN][1000 genomes]
rs225708	0.96[ASN][1000 genomes]
rs225709	0.95[ASN][1000 genomes]
rs225710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs225728	0.82[ASN][1000 genomes]
rs4896574	0.89[CEU][hapmap];0.91[JPT][hapmap]
rs4896575	0.86[CEU][hapmap];0.91[JPT][hapmap]
rs56185739	0.99[ASN][1000 genomes]
rs62430473	0.92[ASN][1000 genomes]
rs62430506	0.84[ASN][1000 genomes]
rs628311	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs638804	0.88[ASN][1000 genomes]
rs639658	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6939944	0.80[ASN][1000 genomes]
rs6939975	0.80[ASN][1000 genomes]
rs7776318	0.81[JPT][hapmap]
rs9321861	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9389979	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs9389980	0.92[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142470200-142488200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:142470200-142488200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:142470200-142491800	Weak transcription	Fetal Stomach	stomach
4	chr6:142470200-142493600	Weak transcription	HSMMtube	muscle
5	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
6	chr6:142472400-142488200	Weak transcription	Primary B cells from cord blood	blood
7	chr6:142474600-142500800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:142474800-142506800	Weak transcription	Hela-S3	cervix
9	chr6:142477200-142500600	Weak transcription	Fetal Brain Male	brain
10	chr6:142477400-142488600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:142477600-142488200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:142477600-142499600	Weak transcription	Stomach Mucosa	stomach
13	chr6:142477800-142491800	Weak transcription	NHLF	lung
14	chr6:142479400-142491800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:142481400-142494400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:142481600-142497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:142481800-142488200	Weak transcription	Right Ventricle	heart
18	chr6:142481800-142488600	Weak transcription	Pancreas	Pancrea
19	chr6:142481800-142495000	Weak transcription	Gastric	stomach
20	chr6:142483200-142499800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:142484000-142488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:142484200-142488200	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:142484200-142488600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:142484200-142533800	Weak transcription	Aorta	Aorta
25	chr6:142484400-142488400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:142484400-142491800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:142484400-142494400	Weak transcription	Fetal Lung	lung
28	chr6:142484400-142498400	Weak transcription	Psoas Muscle	Psoas
29	chr6:142484600-142491000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:142484600-142493400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr6:142484600-142494400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:142484600-142510000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:142485400-142488400	Weak transcription	NH-A	brain
34	chr6:142486000-142488200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:142486400-142488200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:142486400-142495000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:142486400-142497800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:142486600-142488200	Weak transcription	Brain Angular Gyrus	brain
39	chr6:142486600-142493600	Weak transcription	Fetal Kidney	kidney
40	chr6:142486600-142494400	Weak transcription	HMEC	breast
41	chr6:142486600-142498000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:142486800-142488200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:142486800-142488200	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:142486800-142488200	Weak transcription	K562	blood
45	chr6:142486800-142488600	Weak transcription	Fetal Heart	heart
46	chr6:142486800-142492800	Weak transcription	Brain Substantia Nigra	brain
47	chr6:142486800-142496200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:142486800-142497800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:142487000-142489600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:142487000-142496200	Strong transcription	Fetal Thymus	thymus

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