Variant report

Variant	rs2117548
Chromosome Location	chr3:191103462-191103463
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10513865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369278	0.87[CEU][hapmap];0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs1369279	0.87[CEU][hapmap];0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs1474188	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16822368	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16822380	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16822451	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16822489	0.87[CEU][hapmap]
rs16848976	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16866501	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16866503	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16866506	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1715641	0.83[CHB][hapmap]
rs2293379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247189	0.81[ASN][1000 genomes]
rs4247190	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs4677633	0.96[ASN][1000 genomes]
rs4677731	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57369465	0.81[ASN][1000 genomes]
rs57831251	0.81[ASN][1000 genomes]
rs58077600	0.87[ASN][1000 genomes]
rs58596458	0.81[ASN][1000 genomes]
rs58631024	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58648691	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59491001	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60089463	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60176909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60204557	0.87[ASN][1000 genomes]
rs9812544	0.97[ASN][1000 genomes]
rs9832656	0.95[ASN][1000 genomes]
rs9838800	0.95[ASN][1000 genomes]
rs9844500	0.95[ASN][1000 genomes]
rs9854318	0.95[ASN][1000 genomes]
rs9854581	0.96[ASN][1000 genomes]

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	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
2	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:191079600-191121200	Weak transcription	Gastric	stomach
5	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
7	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:191087800-191109200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:191088000-191109800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
14	chr3:191094800-191114800	Weak transcription	A549	lung
15	chr3:191095000-191107600	Weak transcription	Fetal Intestine Small	intestine
16	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:191096400-191109600	Weak transcription	Brain Angular Gyrus	brain
18	chr3:191096600-191105800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:191096600-191114800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:191097200-191109200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:191098000-191111400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:191099400-191107000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
24	chr3:191099600-191113800	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:191099600-191114000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:191099600-191114600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:191099800-191104200	Weak transcription	HepG2	liver
29	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:191100200-191106000	Weak transcription	Left Ventricle	heart
31	chr3:191100200-191106800	Weak transcription	Brain Germinal Matrix	brain
32	chr3:191100200-191107200	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:191100200-191108200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:191100200-191108400	Weak transcription	Ovary	ovary
35	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
36	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
37	chr3:191100200-191119600	Weak transcription	K562	blood
38	chr3:191100400-191107200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:191100400-191108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:191100400-191114000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
42	chr3:191100400-191117400	Weak transcription	Lung	lung
43	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
44	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
45	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
46	chr3:191100600-191107200	Weak transcription	Aorta	Aorta
47	chr3:191100600-191107400	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:191100600-191109400	Weak transcription	Primary T cells from cord blood	blood
49	chr3:191100800-191115400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:191101000-191107400	Weak transcription	Placenta	Placenta

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