Variant report

Variant	rs2635429
Chromosome Location	chr4:143243556-143243557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13144939	1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs1489577	0.80[CEU][hapmap]
rs1489578	1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs1497389	1.00[LWK][hapmap]
rs17715707	1.00[YRI][hapmap]
rs1907105	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs2627802	1.00[LWK][hapmap]
rs2627804	1.00[LWK][hapmap]
rs2627806	0.82[EUR][1000 genomes]
rs2627818	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2627820	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2636671	0.95[GIH][hapmap]
rs2646085	1.00[YRI][hapmap]
rs2646091	1.00[YRI][hapmap]
rs3775716	1.00[YRI][hapmap]
rs6820232	1.00[YRI][hapmap]
rs881611	0.80[CEU][hapmap]
rs931419	1.00[YRI][hapmap]

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
rs2635429	C4orf49	cis	cerebellum	SCAN
rs2635429	LSM6	cis	cerebellum	SCAN

Chromatin state (count:33 , 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	chr4:143235000-143244200	Weak transcription	NHDF-Ad	bronchial
5	chr4:143235600-143266400	Weak transcription	NHEK	skin
6	chr4:143236000-143252000	Weak transcription	HSMM	muscle
7	chr4:143236200-143245600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:143236200-143257000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:143236200-143257200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:143236200-143257600	Weak transcription	HMEC	breast
11	chr4:143236400-143244000	Weak transcription	Dnd41	blood
12	chr4:143236400-143247400	Weak transcription	Fetal Intestine Small	intestine
13	chr4:143237200-143251200	Weak transcription	Stomach Mucosa	stomach
14	chr4:143237400-143244000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:143237400-143252000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:143237600-143251000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:143238200-143244200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:143240200-143245400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:143240200-143246600	Weak transcription	HSMMtube	muscle
20	chr4:143240400-143257000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:143241000-143244200	Weak transcription	Primary T cells from cord blood	blood
22	chr4:143241000-143244800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:143241000-143245200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:143241000-143245400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:143241400-143245600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:143241600-143245200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:143241600-143245600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:143242000-143243600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:143242600-143245600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:143243000-143245600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:143243000-143246800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:143243400-143244600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr4:143243400-143245800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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