Variant report

Variant	rs2646095
Chromosome Location	chr4:143257240-143257241
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11938760	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs13132760	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1391095	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap]
rs1391097	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap]
rs1497386	0.85[CEU][hapmap]
rs1497388	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs17016027	1.00[CHB][hapmap]
rs1872294	0.84[CEU][hapmap]
rs2029990	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2130253	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs2646094	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775707	0.82[MEX][hapmap]
rs6838117	0.84[CEU][hapmap]
rs6844681	0.83[ASW][hapmap]
rs977619	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2646095	ZNF827	cis	cerebellum	SCAN
rs2646095	SCOC	cis	parietal	SCAN
rs2646095	ZNF827	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143217600-143260800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:143234800-143271800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:143235600-143266400	Weak transcription	NHEK	skin
4	chr4:143236200-143257600	Weak transcription	HMEC	breast
5	chr4:143245600-143257600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:143246600-143267800	Weak transcription	Primary T cells from cord blood	blood
7	chr4:143252600-143257400	Weak transcription	Right Ventricle	heart
8	chr4:143253000-143260200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:143253400-143257400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:143253600-143262600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:143254000-143257800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:143255600-143260000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:143255600-143265800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:143256000-143259400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:143256200-143258600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr4:143256200-143269200	Weak transcription	HSMMtube	muscle
17	chr4:143256400-143257600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:143256600-143257800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:143256800-143257800	ZNF genes & repeats	HSMM	muscle
20	chr4:143256800-143258000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:143256800-143258200	ZNF genes & repeats	Dnd41	blood
22	chr4:143256800-143260000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:143256800-143269800	Weak transcription	NHDF-Ad	bronchial
24	chr4:143257000-143257400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:143257000-143257600	ZNF genes & repeats	Fetal Lung	lung
26	chr4:143257000-143257800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:143257000-143258000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:143257000-143258000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr4:143257000-143258000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr4:143257000-143258000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr4:143257000-143258000	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr4:143257200-143257400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr4:143257200-143257600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:143257200-143258000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:143257200-143258000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:143257200-143258000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:143257200-143258000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:143257200-143258000	ZNF genes & repeats	Left Ventricle	heart
39	chr4:143257200-143260000	Weak transcription	Gastric	stomach
40	chr4:143257200-143262800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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