Variant report

Variant	rs3789597
Chromosome Location	chr1:114256139-114256140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10776773	0.83[ASN][1000 genomes]
rs10858015	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102667	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11102678	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1146183	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1146184	0.95[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1146185	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12138638	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12144309	0.84[GIH][hapmap]
rs1217375	1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1217382	0.90[JPT][hapmap]
rs1217393	0.91[JPT][hapmap]
rs1217397	0.90[JPT][hapmap]
rs1217401	0.90[JPT][hapmap]
rs1217403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1217406	0.82[LWK][hapmap];0.83[YRI][hapmap]
rs1217408	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1217414	0.85[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap]
rs1217418	0.82[LWK][hapmap]
rs1217419	0.82[LWK][hapmap]
rs1217423	0.82[JPT][hapmap]
rs1230673	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1230681	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1230684	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1235000	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap]
rs12757859	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13524	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1624335	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap]
rs1743594	0.86[CEU][hapmap];0.97[GIH][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1743595	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1746857	0.89[ASN][1000 genomes]
rs1746860	0.90[JPT][hapmap]
rs1935836	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1970559	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap]
rs2040041	0.85[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs2185827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2476599	0.86[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs2476602	1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap]
rs2636000	0.89[ASN][1000 genomes]
rs2636003	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3789600	0.82[LWK][hapmap]
rs7543121	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs971173	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
2	chr1:114216200-114279800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:114220400-114263800	Weak transcription	Fetal Kidney	kidney
4	chr1:114227000-114268200	Weak transcription	NHLF	lung
5	chr1:114228000-114287800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:114236400-114300000	Weak transcription	Small Intestine	intestine
7	chr1:114237400-114256600	Weak transcription	Colonic Mucosa	Colon
8	chr1:114238000-114258200	Weak transcription	Fetal Heart	heart
9	chr1:114238200-114264400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:114238400-114266800	Weak transcription	NHEK	skin
11	chr1:114239000-114260400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:114239200-114279800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:114239400-114258600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:114240200-114260800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:114240200-114279400	Weak transcription	Psoas Muscle	Psoas
16	chr1:114242000-114300000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:114242200-114256200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:114242200-114256200	Weak transcription	Right Ventricle	heart
19	chr1:114242200-114256200	Weak transcription	A549	lung
20	chr1:114242200-114256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:114242200-114256400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:114242200-114256400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:114242200-114256400	Weak transcription	Aorta	Aorta
24	chr1:114242200-114256400	Weak transcription	Spleen	Spleen
25	chr1:114242200-114256600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:114242200-114258800	Weak transcription	Brain Substantia Nigra	brain
27	chr1:114242200-114260200	Weak transcription	Esophagus	oesophagus
28	chr1:114242200-114260800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:114242200-114260800	Weak transcription	Fetal Lung	lung
30	chr1:114242200-114260800	Weak transcription	Ovary	ovary
31	chr1:114242200-114261000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:114242200-114261200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:114242200-114261200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:114242400-114256200	Weak transcription	Brain Germinal Matrix	brain
35	chr1:114242400-114256200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:114242800-114269800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:114245400-114258000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:114245400-114270800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:114245400-114275000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:114245600-114300600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:114245800-114261200	Weak transcription	Primary T cells from cord blood	blood
42	chr1:114246000-114257400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:114246000-114259800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:114246000-114260200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:114246200-114257200	Strong transcription	HUVEC	blood vessel
46	chr1:114246200-114257600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:114246400-114257600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:114246400-114258800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:114246600-114257600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:114246800-114257400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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