Variant report

Variant	rs6458041
Chromosome Location	chr6:38076216-38076217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10456458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12194275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12206712	0.81[CHB][hapmap]
rs12214320	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12661200	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967149	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2201645	0.81[EUR][1000 genomes]
rs2295791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259679	0.81[CHB][hapmap]
rs2645117	0.81[CHB][hapmap]
rs2645124	0.80[CEU][hapmap]
rs2842505	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4541739	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711523	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs4714117	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4714120	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6925864	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs735117	0.81[CHB][hapmap]
rs909998	0.81[CHB][hapmap]
rs9470813	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr6:38035000-38084000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:38045800-38079800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:38046000-38084200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:38049200-38077400	Weak transcription	Fetal Intestine Small	intestine
7	chr6:38049400-38084400	Weak transcription	Hela-S3	cervix
8	chr6:38051600-38078200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:38052800-38083800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:38052800-38084000	Weak transcription	Dnd41	blood
11	chr6:38053000-38078200	Weak transcription	Fetal Intestine Large	intestine
12	chr6:38053000-38084000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:38053000-38090400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:38053200-38078200	Weak transcription	Fetal Thymus	thymus
15	chr6:38053200-38078200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:38053200-38080000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:38053200-38084000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:38054200-38080000	Weak transcription	Psoas Muscle	Psoas
19	chr6:38054400-38084000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr6:38054600-38084000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:38055600-38084400	Weak transcription	Adipose Nuclei	Adipose
22	chr6:38055800-38084200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:38057200-38109200	Weak transcription	K562	blood
24	chr6:38059800-38077800	Weak transcription	Brain Anterior Caudate	brain
25	chr6:38059800-38091600	Weak transcription	Spleen	Spleen
26	chr6:38060000-38092000	Weak transcription	Aorta	Aorta
27	chr6:38060000-38099400	Weak transcription	Right Ventricle	heart
28	chr6:38060000-38108200	Weak transcription	Ovary	ovary
29	chr6:38060200-38078200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:38060600-38078400	Weak transcription	Brain Angular Gyrus	brain
31	chr6:38061200-38078000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:38061600-38078200	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:38061800-38076400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:38063400-38078000	Weak transcription	HSMMtube	muscle
35	chr6:38063400-38083600	Weak transcription	HepG2	liver
36	chr6:38063400-38085600	Weak transcription	A549	lung
37	chr6:38063600-38077600	Weak transcription	NHLF	lung
38	chr6:38063600-38078200	Weak transcription	HSMM	muscle
39	chr6:38063600-38078800	Weak transcription	Osteobl	bone
40	chr6:38063800-38078200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:38063800-38078400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:38063800-38078400	Weak transcription	NHDF-Ad	bronchial
43	chr6:38063800-38099000	Weak transcription	NH-A	brain
44	chr6:38067600-38078400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:38068400-38083800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:38068400-38083800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:38068600-38084200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:38068800-38076400	Weak transcription	Primary B cells from cord blood	blood
49	chr6:38068800-38078400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:38069200-38078400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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