Variant report

Variant	rs860457
Chromosome Location	chr5:142688323-142688324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10052957	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10482633	0.82[GIH][hapmap]
rs10482642	0.85[GIH][hapmap]
rs10482689	0.85[GIH][hapmap]
rs10515521	0.82[GIH][hapmap]
rs11740792	0.82[GIH][hapmap]
rs11747997	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[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	0.80[EUR][1000 genomes]
rs1635475	0.84[ASN][1000 genomes]
rs17339831	0.85[GIH][hapmap]
rs174048	1.00[ASN][1000 genomes]
rs174050	1.00[ASN][1000 genomes]
rs1837262	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1866388	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs190488	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]
rs2043840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs258748	1.00[ASN][1000 genomes]
rs258750	0.87[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs258751	1.00[ASN][1000 genomes]
rs258752	0.84[ASN][1000 genomes]
rs258753	0.80[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs258754	0.81[EUR][1000 genomes]
rs258755	0.81[EUR][1000 genomes]
rs258757	0.82[ASN][1000 genomes]
rs258813	0.82[ASW][hapmap];0.87[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs258814	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918415	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2918416	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2918417	0.93[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2918418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2918419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2963148	0.95[ASN][1000 genomes]
rs2963149	0.87[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2963150	0.95[ASN][1000 genomes]
rs2963151	1.00[JPT][hapmap]
rs2963153	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2963154	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs33380	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4128428	0.82[GIH][hapmap]
rs6188	0.87[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6196	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6198	0.82[GIH][hapmap]
rs6861962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs712189	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs72801090	0.91[ASN][1000 genomes]
rs852975	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs852977	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs852978	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852979	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs852982	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.85[JPT][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];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs860458	1.00[ASN][1000 genomes]
rs864082	1.00[CHB][hapmap];1.00[CHD][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[CHD][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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142655800-142699200	Strong transcription	Dnd41	blood
2	chr5:142657800-142695400	Weak transcription	Pancreas	Pancrea
3	chr5:142658200-142694800	Weak transcription	Right Ventricle	heart
4	chr5:142658400-142714800	Weak transcription	Esophagus	oesophagus
5	chr5:142659800-142692600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:142664400-142693400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:142667400-142688800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:142668600-142688800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:142668800-142693800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:142677600-142697800	Weak transcription	Fetal Brain Male	brain
11	chr5:142678200-142695400	Weak transcription	Gastric	stomach
12	chr5:142678400-142689200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:142678400-142691400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:142678400-142693400	Weak transcription	Aorta	Aorta
15	chr5:142678400-142693400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:142678400-142693600	Weak transcription	Brain Angular Gyrus	brain
17	chr5:142678400-142693800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:142680200-142689000	Weak transcription	Small Intestine	intestine
19	chr5:142680200-142691000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:142680200-142691400	Weak transcription	Ovary	ovary
21	chr5:142680200-142691600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:142680200-142691800	Weak transcription	Brain Substantia Nigra	brain
23	chr5:142680400-142688400	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:142680400-142690800	Weak transcription	HepG2	liver
25	chr5:142681000-142689600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr5:142682000-142691200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:142682400-142689200	Weak transcription	HUVEC	blood vessel
28	chr5:142682600-142698400	Weak transcription	Stomach Mucosa	stomach
29	chr5:142682800-142691400	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:142683200-142693800	Strong transcription	Primary T cells from cord blood	blood
31	chr5:142683200-142693800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr5:142683200-142693800	Strong transcription	Fetal Thymus	thymus
33	chr5:142683400-142693000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr5:142683800-142688600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:142683800-142689400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:142684000-142689200	ZNF genes & repeats	GM12878-XiMat	blood
37	chr5:142684000-142690800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:142684200-142689600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:142684200-142689800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:142684200-142693200	Strong transcription	Liver	Liver
41	chr5:142684200-142697800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:142684400-142693200	Strong transcription	Adipose Nuclei	Adipose
43	chr5:142684400-142693600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:142684600-142691200	Strong transcription	HSMM	muscle
45	chr5:142685000-142692600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:142685000-142693600	Strong transcription	Fetal Intestine Large	intestine
47	chr5:142685000-142694000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr5:142685200-142689000	Strong transcription	HMEC	breast
49	chr5:142685200-142689800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr5:142685200-142690000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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