Variant report

Variant	rs2646085
Chromosome Location	chr4:143264762-143264763
allele	C/G
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:42)

rs_ID	r²[population]
rs1158692	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1158693	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138212	0.90[JPT][hapmap]
rs13144939	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1391098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1489577	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs1489578	0.83[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs1497389	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs1497397	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1497398	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17715707	1.00[YRI][hapmap]
rs1812174	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]
rs1814133	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982966	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2029991	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173209	0.82[AMR][1000 genomes]
rs2255497	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2627806	0.82[AMR][1000 genomes]
rs2627837	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2635421	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635422	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635424	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635429	1.00[YRI][hapmap]
rs2646086	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2646087	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2646089	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2646090	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2646091	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34830426	0.81[AMR][1000 genomes]
rs3775705	0.89[CEU][hapmap]
rs3775716	1.00[YRI][hapmap]
rs3822157	0.89[CEU][hapmap]
rs6820232	1.00[YRI][hapmap]
rs6825345	0.81[AMR][1000 genomes]
rs716762	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724131	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7699598	0.83[AMR][1000 genomes]
rs881611	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs882004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs882005	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs931419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs980808	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143234800-143271800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr4:143235600-143266400	Weak transcription	NHEK	skin
3	chr4:143246600-143267800	Weak transcription	Primary T cells from cord blood	blood
4	chr4:143255600-143265800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:143256200-143269200	Weak transcription	HSMMtube	muscle
6	chr4:143256800-143269800	Weak transcription	NHDF-Ad	bronchial
7	chr4:143257600-143272000	Weak transcription	Right Ventricle	heart
8	chr4:143258000-143265800	Weak transcription	HMEC	breast
9	chr4:143258000-143267000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:143258000-143267000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:143258000-143269200	Weak transcription	Left Ventricle	heart
12	chr4:143258000-143274800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:143258200-143274000	Weak transcription	Dnd41	blood
14	chr4:143260200-143267000	Weak transcription	Small Intestine	intestine
15	chr4:143260200-143269200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:143260200-143272000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:143262000-143269200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr4:143262000-143269200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:143262800-143267000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:143262800-143271600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:143263000-143271600	Weak transcription	HSMM	muscle
22	chr4:143263200-143265400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:143263200-143265600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:143263200-143266600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:143263200-143266800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:143263200-143267000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:143263200-143267000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr4:143263200-143267000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:143263200-143267400	Weak transcription	Fetal Intestine Small	intestine
30	chr4:143263400-143266600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:143264000-143275400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr4:143264200-143265800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:143264200-143267000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr4:143264400-143268000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:143264600-143274400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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