Variant report

Variant	rs56040643
Chromosome Location	chr3:136257463-136257464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1484250	0.80[AFR][1000 genomes]
rs16843991	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28396702	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34165586	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34962604	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35375192	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35644083	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3932048	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4336059	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4402873	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55993001	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56047785	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56125228	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56251259	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59931907	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6439642	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66810260	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6766450	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6769934	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6782151	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6788346	0.82[AFR][1000 genomes]
rs6789541	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6789761	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6799368	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6804194	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6806795	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7612160	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7615706	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7621017	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621970	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7623824	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7627292	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7644471	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7648591	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9809184	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9812319	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9819496	0.84[EUR][1000 genomes]
rs9831321	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9832572	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9834631	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9850383	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9858457	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9866535	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9868120	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
4	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:136220600-136266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:136222400-136266200	Weak transcription	HSMM	muscle
10	chr3:136232000-136263600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:136246600-136286200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
14	chr3:136247400-136270600	Weak transcription	Fetal Thymus	thymus
15	chr3:136247800-136261600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:136251600-136264400	Weak transcription	Fetal Lung	lung
19	chr3:136251600-136266000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:136251600-136270400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:136251600-136284400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:136251600-136284400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:136251600-136289400	Weak transcription	Adipose Nuclei	Adipose
24	chr3:136251600-136322400	Weak transcription	Liver	Liver
25	chr3:136251800-136262200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:136251800-136266400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:136251800-136284800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:136252000-136270000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:136252600-136262400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:136252600-136264600	Weak transcription	Thymus	Thymus
31	chr3:136252600-136266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:136252600-136284800	Weak transcription	Left Ventricle	heart
33	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:136252800-136266000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:136253000-136258000	Weak transcription	Fetal Kidney	kidney
38	chr3:136253000-136262400	Weak transcription	Primary B cells from cord blood	blood
39	chr3:136253600-136264600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:136254400-136265000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:136255000-136258600	Strong transcription	Dnd41	blood
42	chr3:136255200-136294000	Weak transcription	Primary T cells from cord blood	blood
43	chr3:136255400-136261600	Weak transcription	HUVEC	blood vessel
44	chr3:136255600-136258200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:136255800-136291600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:136256600-136263400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:136256800-136263000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:136256800-136266200	Weak transcription	NHDF-Ad	bronchial
49	chr3:136257000-136257600	Strong transcription	Fetal Stomach	stomach
50	chr3:136257000-136258000	Strong transcription	Fetal Intestine Small	intestine

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