Variant report

Variant	rs6196
Chromosome Location	chr5:142661490-142661491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:142655877..142658006-chr5:142659926..142661730,2	K562	blood:
2	chr5:142659505..142662280-chr5:142782348..142785528,3	K562	blood:

Variant related genes	Relation type
ENSG00000113580	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10052957	1.00[JPT][hapmap]
rs10482614	0.85[EUR][1000 genomes]
rs10515522	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs11747997	0.91[ASN][1000 genomes]
rs11749561	1.00[JPT][hapmap]
rs1438732	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635475	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs174048	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174050	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837262	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1866388	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs190488	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2043840	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs258748	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258750	1.00[JPT][hapmap]
rs258751	1.00[ASN][1000 genomes]
rs258752	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs258753	0.85[JPT][hapmap]
rs258757	0.82[ASN][1000 genomes]
rs258813	1.00[JPT][hapmap]
rs258814	1.00[ASN][1000 genomes]
rs2918415	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918416	1.00[JPT][hapmap]
rs2918417	1.00[JPT][hapmap]
rs2918418	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918419	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2963148	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2963149	1.00[JPT][hapmap]
rs2963150	0.95[ASN][1000 genomes]
rs2963151	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2963154	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33380	0.95[ASN][1000 genomes]
rs33381	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33382	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33389	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423247	0.82[AFR][1000 genomes]
rs55817235	0.82[EUR][1000 genomes]
rs56150733	0.82[EUR][1000 genomes]
rs61752263	0.81[EUR][1000 genomes]
rs6188	1.00[JPT][hapmap]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6861962	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs712189	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72801054	0.92[EUR][1000 genomes]
rs72801080	0.81[EUR][1000 genomes]
rs72801090	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72801096	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs852977	1.00[JPT][hapmap]
rs852978	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852979	0.98[ASN][1000 genomes]
rs852982	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs852984	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853154	0.82[EUR][1000 genomes]
rs853156	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853157	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853176	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs853177	0.85[EUR][1000 genomes]
rs853178	0.85[EUR][1000 genomes]
rs853179	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853182	1.00[ASN][1000 genomes]
rs853184	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860457	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs860458	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860465	0.85[EUR][1000 genomes]
rs862489	0.82[EUR][1000 genomes]
rs864082	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs864355	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs865482	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324918	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv33748	chr5:142638267-142699595	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv5041	chr5:142653189-142697896	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6196	UBE2D2	cis	cerebellum	SCAN
rs6196	STK32A	cis	cerebellum	SCAN
rs6196	PAIP2	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142646600-142672400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:142650000-142674000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:142650600-142677200	Weak transcription	Aorta	Aorta
4	chr5:142652200-142669800	Weak transcription	Left Ventricle	heart
5	chr5:142653000-142671200	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:142653200-142674800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:142654600-142666600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:142654800-142663600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:142655000-142664800	Weak transcription	NHEK	skin
10	chr5:142655000-142669800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:142655000-142671600	Weak transcription	K562	blood
12	chr5:142655200-142662400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:142655200-142674000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:142655200-142674200	Weak transcription	Brain Angular Gyrus	brain
15	chr5:142655400-142672600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:142655800-142662000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:142655800-142664600	Strong transcription	NHDF-Ad	bronchial
18	chr5:142655800-142669800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:142655800-142670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:142655800-142671800	Weak transcription	Psoas Muscle	Psoas
21	chr5:142655800-142677200	Weak transcription	Spleen	Spleen
22	chr5:142655800-142699200	Strong transcription	Dnd41	blood
23	chr5:142656000-142664000	Strong transcription	HSMM	muscle
24	chr5:142656000-142677400	Weak transcription	Gastric	stomach
25	chr5:142656400-142664400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:142656600-142671600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:142656600-142677000	Weak transcription	Lung	lung
28	chr5:142656800-142661800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:142656800-142663600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:142657000-142663400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:142657000-142664400	Strong transcription	HMEC	breast
32	chr5:142657000-142674000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:142657600-142663400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:142657800-142662600	Strong transcription	Primary T cells from cord blood	blood
35	chr5:142657800-142663400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:142657800-142667800	Weak transcription	Fetal Stomach	stomach
37	chr5:142657800-142671800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr5:142657800-142695400	Weak transcription	Pancreas	Pancrea
39	chr5:142658000-142664000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:142658000-142664000	Strong transcription	Fetal Thymus	thymus
41	chr5:142658000-142665000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr5:142658000-142665200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:142658000-142679000	Weak transcription	Colonic Mucosa	Colon
44	chr5:142658200-142662000	Weak transcription	Fetal Intestine Small	intestine
45	chr5:142658200-142663200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:142658200-142663600	Strong transcription	Adipose Nuclei	Adipose
47	chr5:142658200-142663600	Weak transcription	Brain Substantia Nigra	brain
48	chr5:142658200-142663800	Weak transcription	Fetal Heart	heart
49	chr5:142658200-142664800	Strong transcription	Osteobl	bone
50	chr5:142658200-142665000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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