Variant report

Variant	rs9462380
Chromosome Location	chr6:38065123-38065124
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	chr6:38060436..38062438-chr6:38064379..38067243,2	K562	blood:
2	chr6:38062824..38065350-chr6:38071791..38074168,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10755700	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13198420	0.84[CHB][hapmap]
rs1885325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1923279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1979759	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2201646	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs259672	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259675	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259676	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259678	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259683	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259687	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs259693	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4506034	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711522	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711524	0.84[EUR][1000 genomes]
rs4714123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4714125	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6458040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6458042	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916091	0.94[ASN][1000 genomes]
rs6924634	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6929371	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6930859	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6936504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6938580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7751390	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765798	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs881681	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9349053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9369029	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9369033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9380716	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394471	0.87[EUR][1000 genomes]
rs9462374	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9470762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9470767	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470800	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

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:80 , 50 per page) page: 1 2

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	chr6:38036400-38075000	Weak transcription	Thymus	Thymus
4	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:38045800-38079800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:38046000-38084200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:38046600-38074200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:38047600-38076200	Weak transcription	Fetal Stomach	stomach
9	chr6:38048000-38073000	Weak transcription	Small Intestine	intestine
10	chr6:38049200-38072600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:38049200-38077400	Weak transcription	Fetal Intestine Small	intestine
12	chr6:38049400-38084400	Weak transcription	Hela-S3	cervix
13	chr6:38051200-38066800	Weak transcription	GM12878-XiMat	blood
14	chr6:38051400-38074800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:38051400-38076200	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:38051600-38067800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:38051600-38076200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:38051600-38078200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:38052000-38074800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:38052800-38083800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:38052800-38084000	Weak transcription	Dnd41	blood
22	chr6:38053000-38075800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:38053000-38078200	Weak transcription	Fetal Intestine Large	intestine
24	chr6:38053000-38084000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:38053000-38090400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:38053200-38078200	Weak transcription	Fetal Thymus	thymus
27	chr6:38053200-38078200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:38053200-38080000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr6:38053200-38084000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:38054200-38080000	Weak transcription	Psoas Muscle	Psoas
31	chr6:38054400-38068000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr6:38054400-38084000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:38054600-38084000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:38055000-38068200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:38055000-38074000	Weak transcription	Liver	Liver
36	chr6:38055000-38075000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:38055200-38072800	Weak transcription	Primary T cells from cord blood	blood
38	chr6:38055600-38072600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:38055600-38074200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr6:38055600-38084400	Weak transcription	Adipose Nuclei	Adipose
41	chr6:38055800-38084200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:38056000-38071800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:38057200-38109200	Weak transcription	K562	blood
44	chr6:38059400-38074800	Weak transcription	Fetal Lung	lung
45	chr6:38059800-38076200	Weak transcription	Lung	lung
46	chr6:38059800-38077800	Weak transcription	Brain Anterior Caudate	brain
47	chr6:38059800-38091600	Weak transcription	Spleen	Spleen
48	chr6:38060000-38092000	Weak transcription	Aorta	Aorta
49	chr6:38060000-38099400	Weak transcription	Right Ventricle	heart
50	chr6:38060000-38108200	Weak transcription	Ovary	ovary

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