Variant report

Variant	rs190488
Chromosome Location	chr5:142670308-142670309
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10052957	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11747997	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11749561	1.00[JPT][hapmap]
rs1438732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1635474	0.82[EUR][1000 genomes]
rs1635475	0.84[ASN][1000 genomes]
rs174048	1.00[ASN][1000 genomes]
rs174050	1.00[ASN][1000 genomes]
rs1837262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1866388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2043840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs258748	1.00[ASN][1000 genomes]
rs258750	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs258751	1.00[ASN][1000 genomes]
rs258752	0.84[ASN][1000 genomes]
rs258753	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs258754	0.83[EUR][1000 genomes]
rs258755	0.82[EUR][1000 genomes]
rs258757	0.82[ASN][1000 genomes]
rs258813	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs258814	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2918416	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2918417	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2918418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2918419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2963148	0.95[ASN][1000 genomes]
rs2963149	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2963150	0.95[ASN][1000 genomes]
rs2963151	1.00[JPT][hapmap]
rs2963153	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2963154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs33380	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33381	0.95[ASN][1000 genomes]
rs33382	0.95[ASN][1000 genomes]
rs33389	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6188	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6861962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs712189	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs72801090	0.91[ASN][1000 genomes]
rs852975	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs852977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs852978	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852979	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs852982	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs852984	0.95[ASN][1000 genomes]
rs853156	0.84[ASN][1000 genomes]
rs853157	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs853176	0.85[ASN][1000 genomes]
rs853179	0.87[ASN][1000 genomes]
rs853182	1.00[ASN][1000 genomes]
rs853184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs860457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860458	1.00[ASN][1000 genomes]
rs864082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs864355	0.87[ASN][1000 genomes]
rs865482	1.00[ASN][1000 genomes]
rs9324918	1.00[CHB][hapmap];1.00[JPT][hapmap];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

No data

Chromatin state (count:106 , 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	chr5:142653000-142671200	Weak transcription	Brain Hippocampus Middle	brain
5	chr5:142653200-142674800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:142655000-142671600	Weak transcription	K562	blood
7	chr5:142655200-142674000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:142655200-142674200	Weak transcription	Brain Angular Gyrus	brain
9	chr5:142655400-142672600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:142655800-142671800	Weak transcription	Psoas Muscle	Psoas
11	chr5:142655800-142677200	Weak transcription	Spleen	Spleen
12	chr5:142655800-142699200	Strong transcription	Dnd41	blood
13	chr5:142656000-142677400	Weak transcription	Gastric	stomach
14	chr5:142656600-142671600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:142656600-142677000	Weak transcription	Lung	lung
16	chr5:142657000-142674000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr5:142657800-142671800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:142657800-142695400	Weak transcription	Pancreas	Pancrea
19	chr5:142658000-142679000	Weak transcription	Colonic Mucosa	Colon
20	chr5:142658200-142671400	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:142658200-142694800	Weak transcription	Right Ventricle	heart
22	chr5:142658400-142714800	Weak transcription	Esophagus	oesophagus
23	chr5:142658800-142677400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:142659400-142677200	Weak transcription	HSMMtube	muscle
25	chr5:142659600-142674600	Weak transcription	HepG2	liver
26	chr5:142659600-142677400	Weak transcription	Ovary	ovary
27	chr5:142659800-142679400	Weak transcription	Small Intestine	intestine
28	chr5:142659800-142692600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:142660200-142670400	Weak transcription	Brain Anterior Caudate	brain
30	chr5:142661600-142677200	Weak transcription	HUVEC	blood vessel
31	chr5:142661800-142671200	Weak transcription	Hela-S3	cervix
32	chr5:142662400-142673000	Weak transcription	NH-A	brain
33	chr5:142662600-142672800	Weak transcription	Fetal Kidney	kidney
34	chr5:142663800-142670400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr5:142663800-142671200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:142663800-142671200	Weak transcription	NHLF	lung
37	chr5:142664000-142671400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:142664000-142671400	Weak transcription	HSMM	muscle
39	chr5:142664000-142672000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:142664000-142672200	Weak transcription	Fetal Heart	heart
41	chr5:142664000-142673800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:142664000-142674000	Weak transcription	Brain Substantia Nigra	brain
43	chr5:142664000-142677400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr5:142664000-142684600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:142664000-142685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:142664200-142674600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:142664400-142670400	Weak transcription	HMEC	breast
48	chr5:142664400-142671000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:142664400-142671400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:142664400-142671400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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