Variant report

Variant	rs295491
Chromosome Location	chr3:139243460-139243461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10935330	1.00[CEU][hapmap]
rs1599744	1.00[CHD][hapmap]
rs167186	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16849083	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs176986	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs176988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211583	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295495	1.00[CEU][hapmap];0.84[GIH][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.84[AFR][1000 genomes]
rs4525826	0.85[AMR][1000 genomes]
rs55735000	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56265838	0.85[AMR][1000 genomes]
rs60144275	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61525084	0.92[AFR][1000 genomes]
rs6439851	0.85[AMR][1000 genomes]
rs6788313	1.00[JPT][hapmap]
rs72988746	0.82[EUR][1000 genomes]
rs7372667	1.00[JPT][hapmap]
rs7372737	0.85[AMR][1000 genomes]
rs73868351	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7621965	0.85[AMR][1000 genomes]
rs893704	0.82[LWK][hapmap]
rs9824044	0.85[AMR][1000 genomes]
rs9824195	0.85[AMR][1000 genomes]
rs9838015	0.85[AMR][1000 genomes]
rs9864352	0.85[AMR][1000 genomes]
rs9864740	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139223000-139247000	Weak transcription	Left Ventricle	heart
3	chr3:139228600-139245000	Weak transcription	Spleen	Spleen
4	chr3:139228800-139253200	Weak transcription	Gastric	stomach
5	chr3:139231000-139252800	Weak transcription	Right Ventricle	heart
6	chr3:139232400-139244400	Weak transcription	HSMMtube	muscle
7	chr3:139234400-139252600	Weak transcription	Lung	lung
8	chr3:139234800-139250600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:139234800-139251000	Weak transcription	Fetal Kidney	kidney
10	chr3:139234800-139251200	Weak transcription	Fetal Heart	heart
11	chr3:139235000-139253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:139235200-139251400	Weak transcription	Liver	Liver
13	chr3:139236000-139245200	Weak transcription	Brain Anterior Caudate	brain
14	chr3:139236400-139250800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:139236600-139245000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:139236600-139252000	Weak transcription	Right Atrium	heart
17	chr3:139237200-139249600	Weak transcription	Brain Germinal Matrix	brain
18	chr3:139238800-139251600	Weak transcription	Small Intestine	intestine
19	chr3:139239000-139245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:139239000-139247600	Weak transcription	NHEK	skin
21	chr3:139239000-139249600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:139239200-139244800	Weak transcription	Fetal Lung	lung
23	chr3:139239200-139247400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:139239200-139251400	Weak transcription	Placenta	Placenta
25	chr3:139239400-139246400	Weak transcription	Esophagus	oesophagus
26	chr3:139239600-139244000	Weak transcription	Fetal Intestine Large	intestine
27	chr3:139239600-139250000	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:139239600-139250000	Weak transcription	Brain Substantia Nigra	brain
29	chr3:139239600-139251400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:139240600-139248600	Strong transcription	NH-A	brain
31	chr3:139240600-139251000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:139240800-139251800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:139241200-139245400	Weak transcription	Fetal Brain Female	brain
34	chr3:139241400-139251200	Strong transcription	Fetal Intestine Small	intestine
35	chr3:139241400-139251200	Strong transcription	Fetal Stomach	stomach
36	chr3:139241400-139253200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:139241600-139247600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:139241800-139245000	Weak transcription	Pancreas	Pancrea
39	chr3:139242000-139243800	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:139242000-139244200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
41	chr3:139242200-139244000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:139242200-139244200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
43	chr3:139242200-139245000	Weak transcription	Aorta	Aorta
44	chr3:139242400-139243600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr3:139242400-139243600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr3:139242400-139244000	Weak transcription	Ovary	ovary
47	chr3:139242400-139244400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:139242400-139244400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:139242600-139243800	Enhancers	H9 Cell Line	embryonic stem cell
50	chr3:139242600-139243800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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