Variant report

Variant	rs2627802
Chromosome Location	chr4:143256597-143256598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1158692	0.86[GIH][hapmap]
rs13144939	1.00[LWK][hapmap]
rs1489578	1.00[LWK][hapmap]
rs1497389	1.00[LWK][hapmap]
rs1994555	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2627804	1.00[LWK][hapmap]
rs2627814	0.93[EUR][1000 genomes]
rs2635424	0.86[GIH][hapmap]
rs2635425	0.93[EUR][1000 genomes]
rs2635426	0.94[EUR][1000 genomes]
rs2635427	0.88[EUR][1000 genomes]
rs2635428	0.92[EUR][1000 genomes]
rs2635429	1.00[LWK][hapmap]
rs2636671	1.00[ASW][hapmap];0.89[MKK][hapmap];0.81[EUR][1000 genomes]
rs2646088	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2646096	0.93[EUR][1000 genomes]
rs6844681	0.93[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs716762	0.86[GIH][hapmap]
rs882032	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs960679	0.80[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2627802	C4orf49	cis	cerebellum	SCAN
rs2627802	NDUFC1	cis	parietal	SCAN

Chromatin state (count:38 , 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	chr4:143233800-143257200	Weak transcription	Left Ventricle	heart
3	chr4:143234800-143271800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:143235600-143266400	Weak transcription	NHEK	skin
5	chr4:143236200-143257000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:143236200-143257200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:143236200-143257600	Weak transcription	HMEC	breast
8	chr4:143240400-143257000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:143244400-143256800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:143244600-143256800	Weak transcription	Dnd41	blood
11	chr4:143245600-143257600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:143245800-143257200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:143246000-143257000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:143246600-143267800	Weak transcription	Primary T cells from cord blood	blood
15	chr4:143246800-143257200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:143250800-143256800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:143252600-143257000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr4:143252600-143257200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:143252600-143257400	Weak transcription	Right Ventricle	heart
20	chr4:143252800-143257000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:143253000-143260200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:143253200-143257000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:143253400-143257400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:143253600-143257000	Weak transcription	Fetal Lung	lung
25	chr4:143253600-143262600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:143254000-143257800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:143255000-143256600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:143255200-143256800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:143255600-143260000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:143255600-143265800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr4:143255800-143256800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:143256000-143256800	Weak transcription	HSMM	muscle
33	chr4:143256000-143257000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:143256000-143259400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr4:143256200-143256600	Weak transcription	NHDF-Ad	bronchial
36	chr4:143256200-143258600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr4:143256200-143269200	Weak transcription	HSMMtube	muscle
38	chr4:143256400-143257600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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