Variant report

Variant	rs225673
Chromosome Location	chr6:142506290-142506291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11758623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs178783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225601	0.93[ASN][1000 genomes]
rs225602	0.93[ASN][1000 genomes]
rs225604	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs225606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs225618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225620	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225623	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225624	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225629	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225633	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225634	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs225635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225636	0.96[ASN][1000 genomes]
rs225639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225640	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225650	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225651	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225655	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225656	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs225657	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs225658	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs225659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225661	0.92[ASN][1000 genomes]
rs225662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs225664	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225667	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225668	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225670	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225672	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225677	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225678	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]
rs225679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225680	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225682	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225683	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225688	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs225689	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225690	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225692	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225693	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225696	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225697	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225698	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225701	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225704	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225705	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225706	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225707	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225708	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225709	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225728	0.83[ASN][1000 genomes]
rs4896574	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4896575	0.91[JPT][hapmap]
rs56185739	1.00[ASN][1000 genomes]
rs62430473	0.93[ASN][1000 genomes]
rs62430506	0.85[ASN][1000 genomes]
rs628311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs638804	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7776318	0.81[JPT][hapmap]
rs9321861	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9389979	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9389980	0.92[CHB][hapmap];0.82[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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142474800-142506800	Weak transcription	Hela-S3	cervix
2	chr6:142484200-142533800	Weak transcription	Aorta	Aorta
3	chr6:142484600-142510000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:142489000-142543200	Weak transcription	Small Intestine	intestine
5	chr6:142489200-142507400	Weak transcription	Fetal Heart	heart
6	chr6:142492200-142524800	Weak transcription	Brain Angular Gyrus	brain
7	chr6:142495400-142517000	Weak transcription	NHEK	skin
8	chr6:142495600-142510400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:142495600-142513000	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:142495600-142533600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:142495800-142519600	Weak transcription	HMEC	breast
12	chr6:142496000-142525000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:142496000-142528600	Weak transcription	Lung	lung
14	chr6:142496200-142510400	Weak transcription	Fetal Intestine Large	intestine
15	chr6:142496200-142513200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:142496200-142514800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:142496200-142519400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:142496200-142519600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:142496200-142527600	Weak transcription	Thymus	Thymus
20	chr6:142496200-142528200	Weak transcription	Fetal Stomach	stomach
21	chr6:142496200-142528400	Weak transcription	Brain Germinal Matrix	brain
22	chr6:142496200-142533800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:142496200-142533800	Weak transcription	Gastric	stomach
24	chr6:142496200-142533800	Weak transcription	Pancreas	Pancrea
25	chr6:142496400-142517200	Weak transcription	Osteobl	bone
26	chr6:142496400-142528000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:142496400-142533600	Weak transcription	Colonic Mucosa	Colon
28	chr6:142496600-142519600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:142496600-142525800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:142496600-142526200	Weak transcription	Esophagus	oesophagus
31	chr6:142496600-142533800	Weak transcription	Left Ventricle	heart
32	chr6:142496600-142546800	Weak transcription	NHLF	lung
33	chr6:142498200-142526000	Weak transcription	Fetal Intestine Small	intestine
34	chr6:142498400-142510200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:142498600-142510000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:142498600-142519600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:142498600-142527800	Weak transcription	Ovary	ovary
38	chr6:142499000-142510400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:142499200-142510600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:142499200-142524800	Weak transcription	HSMMtube	muscle
41	chr6:142499400-142507400	Weak transcription	A549	lung
42	chr6:142499400-142508200	Weak transcription	HUVEC	blood vessel
43	chr6:142499400-142510200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:142499400-142510200	Weak transcription	HepG2	liver
45	chr6:142499400-142511600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:142499400-142514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:142499400-142514800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:142499400-142514800	Weak transcription	Psoas Muscle	Psoas
49	chr6:142499400-142515800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr6:142499400-142519600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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