Variant report

Variant	rs28445226
Chromosome Location	chr6:38258226-38258227
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1033480	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10947725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947726	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947728	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947729	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11759824	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1205108	1.00[CHB][hapmap]
rs12191714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12201631	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12202804	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12206324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208912	0.92[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12212983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12214470	0.81[ASN][1000 genomes]
rs12215330	0.96[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs12215850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1883610	0.86[JPT][hapmap]
rs1931758	0.92[ASN][1000 genomes]
rs1983605	1.00[JPT][hapmap]
rs2179532	0.84[CEU][hapmap]
rs2179533	0.84[CEU][hapmap]
rs228179	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs228186	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs228188	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4236058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711542	1.00[JPT][hapmap]
rs4711546	1.00[JPT][hapmap]
rs4714148	0.87[CHD][hapmap]
rs4714152	1.00[JPT][hapmap]
rs4714157	1.00[JPT][hapmap]
rs4714165	0.88[JPT][hapmap]
rs6899746	1.00[JPT][hapmap]
rs6901086	1.00[JPT][hapmap]
rs6904723	1.00[JPT][hapmap]
rs6933268	1.00[JPT][hapmap]
rs6933758	1.00[JPT][hapmap]
rs6940319	1.00[JPT][hapmap]
rs742515	1.00[JPT][hapmap]
rs7748599	1.00[JPT][hapmap]
rs7749685	1.00[JPT][hapmap]
rs7759629	1.00[JPT][hapmap]
rs7763775	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7766214	1.00[JPT][hapmap]
rs871183	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9349073	1.00[JPT][hapmap]
rs9357272	1.00[JPT][hapmap]
rs9380743	1.00[JPT][hapmap]
rs9394495	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9470885	1.00[JPT][hapmap]
rs9470888	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38224400-38267600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38239400-38259200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:38248400-38258400	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:38249200-38258400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:38249200-38275600	Weak transcription	Fetal Brain Male	brain
6	chr6:38256000-38258400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:38256000-38263000	Weak transcription	Lung	lung
8	chr6:38256200-38258400	Weak transcription	Ovary	ovary
9	chr6:38256200-38258400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:38256400-38259000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:38257400-38258600	Enhancers	Fetal Heart	heart
12	chr6:38257600-38258600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:38257600-38258600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:38257600-38258600	Enhancers	Brain Anterior Caudate	brain
15	chr6:38257600-38259000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:38257800-38258400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:38257800-38258400	Enhancers	Fetal Kidney	kidney
18	chr6:38257800-38258600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:38257800-38258600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:38257800-38258600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr6:38257800-38258800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr6:38258000-38258400	Enhancers	Brain Angular Gyrus	brain
23	chr6:38258000-38258400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:38258000-38258400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:38258000-38258400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr6:38258000-38258600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr6:38258000-38258600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:38258000-38258600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:38258000-38258600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:38258000-38258600	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:38258000-38258800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr6:38258000-38258800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr6:38258000-38259000	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr6:38258200-38258400	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr6:38258200-38258400	Enhancers	Left Ventricle	heart
36	chr6:38258200-38258400	Enhancers	Rectal Smooth Muscle	rectum
37	chr6:38258200-38258600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr6:38258200-38258600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr6:38258200-38258600	Enhancers	Brain Substantia Nigra	brain
40	chr6:38258200-38258600	Enhancers	Psoas Muscle	Psoas

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