Variant report

Variant	rs12204352
Chromosome Location	chr6:38042940-38042941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456097	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10947712	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12190306	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12190570	0.88[CHB][hapmap]
rs12194618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12194823	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12200258	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12211248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12212723	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12213151	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12213835	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12214375	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs13214465	0.81[EUR][1000 genomes]
rs13220131	0.81[EUR][1000 genomes]
rs1569657	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16890344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2055206	0.80[CEU][hapmap]
rs2132597	0.81[EUR][1000 genomes]
rs2281266	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs259679	0.88[CHB][hapmap]
rs259686	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259691	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2645102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2645107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2645113	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2645117	0.88[CHB][hapmap]
rs2645124	0.85[CHB][hapmap]
rs2645127	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645128	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2645134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2645137	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842500	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2842527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842529	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2842531	1.00[YRI][hapmap]
rs34952988	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35257826	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35823566	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56098839	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56140804	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7747130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs941850	0.88[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38017200-38055000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:38020400-38046200	Weak transcription	Stomach Mucosa	stomach
3	chr6:38023000-38054800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:38023200-38052800	Weak transcription	Gastric	stomach
5	chr6:38024600-38045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:38026000-38047600	Weak transcription	Hela-S3	cervix
7	chr6:38026200-38053800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:38031400-38045000	Weak transcription	Aorta	Aorta
10	chr6:38031400-38052400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:38031600-38048200	Weak transcription	HUVEC	blood vessel
12	chr6:38031600-38048600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:38031600-38049400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:38031600-38053200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:38031600-38059600	Weak transcription	Spleen	Spleen
16	chr6:38031600-38061600	Weak transcription	Brain Germinal Matrix	brain
17	chr6:38031800-38045400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:38032000-38052600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:38032000-38052600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:38032200-38044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:38032200-38048200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:38032200-38048400	Weak transcription	HSMM	muscle
23	chr6:38032200-38048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:38032200-38051400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:38032400-38045200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:38032400-38045400	Weak transcription	A549	lung
27	chr6:38032400-38050800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:38032400-38056200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:38032800-38046400	Weak transcription	Osteobl	bone
30	chr6:38032800-38046600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:38032800-38046800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:38032800-38050000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:38032800-38050000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:38032800-38050000	Weak transcription	Dnd41	blood
35	chr6:38032800-38050000	Weak transcription	NHEK	skin
36	chr6:38033000-38051200	Weak transcription	Fetal Intestine Large	intestine
37	chr6:38033000-38052600	Weak transcription	Lung	lung
38	chr6:38033000-38063400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:38033200-38048400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:38033200-38050000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:38033200-38051000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:38033400-38048200	Weak transcription	NH-A	brain
43	chr6:38033600-38045400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr6:38033600-38050800	Weak transcription	Placenta	Placenta
45	chr6:38034200-38045200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:38034200-38050200	Weak transcription	HSMMtube	muscle
47	chr6:38034200-38051200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:38034600-38045600	Weak transcription	HepG2	liver
49	chr6:38035000-38046600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:38035000-38084000	Weak transcription	Stomach Smooth Muscle	stomach

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