Variant report

Variant	rs9394496
Chromosome Location	chr6:38373280-38373281
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38371909..38373449-chr6:38395704..38397463,2	K562	blood:
2	chr6:38368148..38369962-chr6:38370893..38373695,3	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10484927	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484929	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10484930	1.00[TSI][hapmap]
rs11964070	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12524225	0.89[ASW][hapmap];1.00[TSI][hapmap]
rs12527432	0.89[ASW][hapmap];1.00[TSI][hapmap]
rs12660323	1.00[TSI][hapmap]
rs16890515	1.00[EUR][1000 genomes]
rs16890537	1.00[EUR][1000 genomes]
rs16890552	0.84[GIH][hapmap];1.00[TSI][hapmap]
rs16890561	0.89[ASW][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16890588	0.89[CHB][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16890641	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623233	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs4711531	1.00[TSI][hapmap]
rs4711545	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4714139	1.00[TSI][hapmap]
rs4714154	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55842851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57277481	1.00[EUR][1000 genomes]
rs60405483	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73422889	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73424720	1.00[EUR][1000 genomes]
rs871184	0.80[GIH][hapmap];1.00[TSI][hapmap]
rs9296243	0.89[ASW][hapmap];1.00[TSI][hapmap]
rs9349065	1.00[TSI][hapmap]
rs9349074	0.83[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap]
rs9349080	0.81[ASN][1000 genomes]
rs9357268	0.83[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9366956	0.89[ASW][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs9369047	0.89[ASW][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs9369053	0.83[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs9369056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380738	0.83[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9380744	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380746	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394487	1.00[TSI][hapmap]
rs971876	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38354000-38376000	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38368200-38373600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:38370800-38375200	Enhancers	Fetal Brain Male	brain
4	chr6:38371200-38375600	Enhancers	Adipose Nuclei	Adipose
5	chr6:38371600-38374000	Enhancers	Brain Hippocampus Middle	brain
6	chr6:38371600-38376400	Enhancers	Liver	Liver
7	chr6:38371800-38373400	Enhancers	HepG2	liver
8	chr6:38371800-38374000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:38371800-38374000	Enhancers	HMEC	breast
10	chr6:38371800-38374200	Enhancers	NHEK	skin
11	chr6:38372000-38373400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:38372000-38373400	Enhancers	Brain Cingulate Gyrus	brain
13	chr6:38372000-38373400	Enhancers	Hela-S3	cervix
14	chr6:38372000-38373600	Enhancers	Brain Germinal Matrix	brain
15	chr6:38372000-38374000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:38372000-38374000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:38372000-38374000	Enhancers	Brain Anterior Caudate	brain
18	chr6:38372000-38374000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr6:38372000-38374000	Enhancers	Brain Substantia Nigra	brain
20	chr6:38372000-38374800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:38372200-38373800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:38372200-38373800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr6:38372200-38374000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:38372400-38373400	Enhancers	Fetal Intestine Large	intestine
25	chr6:38372400-38373800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:38372400-38373800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr6:38372400-38374600	Weak transcription	Ovary	ovary
28	chr6:38372600-38373400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:38372600-38373600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:38372600-38373800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:38372600-38375000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:38372800-38374600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:38372800-38376200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:38373000-38373400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:38373000-38373400	Enhancers	A549	lung
36	chr6:38373000-38374000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr6:38373000-38376800	Weak transcription	Aorta	Aorta
38	chr6:38373200-38373800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:38373200-38373800	Weak transcription	Fetal Brain Female	brain
40	chr6:38373200-38374200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:38373200-38374600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:38373200-38374600	Weak transcription	Psoas Muscle	Psoas
43	chr6:38373200-38395600	Weak transcription	Fetal Intestine Small	intestine

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