Variant report

Variant	rs11938760
Chromosome Location	chr4:143290199-143290200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13132760	0.83[ASN][1000 genomes]
rs13133199	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1391095	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1391097	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs1497386	0.83[JPT][hapmap]
rs1497388	0.83[JPT][hapmap];0.91[MEX][hapmap]
rs17016027	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2029990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2130253	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2646095	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs3775707	0.85[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs6838117	0.83[JPT][hapmap]
rs71608480	0.85[ASN][1000 genomes]
rs977619	0.90[AMR][1000 genomes];0.97[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	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
4	nsv292161	chr4:143289470-143290740	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11938760	C4orf49	cis	cerebellum	SCAN
rs11938760	SCOC	cis	parietal	SCAN
rs11938760	ZNF827	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143273400-143299000	Weak transcription	Left Ventricle	heart
2	chr4:143278400-143294200	Weak transcription	Stomach Mucosa	stomach
3	chr4:143285000-143294600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr4:143285200-143290200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:143285200-143298400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr4:143285800-143290400	Enhancers	NHDF-Ad	bronchial
7	chr4:143286000-143290600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:143286200-143290600	Enhancers	HMEC	breast
9	chr4:143286400-143290400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:143286800-143293800	Weak transcription	Osteobl	bone
11	chr4:143287000-143293800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:143288000-143290200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:143288000-143290200	Enhancers	HUVEC	blood vessel
14	chr4:143288000-143290400	Enhancers	Primary hematopoietic stem cells	blood
15	chr4:143288000-143290400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr4:143288000-143290600	Enhancers	Primary T cells from cord blood	blood
17	chr4:143288000-143290600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:143288000-143293400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:143288400-143293800	Weak transcription	Aorta	Aorta
20	chr4:143288800-143290400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:143288800-143296200	Weak transcription	A549	lung
22	chr4:143289000-143290400	Weak transcription	Psoas Muscle	Psoas
23	chr4:143289000-143290600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:143289000-143290600	Enhancers	Dnd41	blood
25	chr4:143289000-143291400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr4:143289000-143293800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:143289000-143293800	Weak transcription	Small Intestine	intestine
28	chr4:143289000-143295200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:143289000-143300600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:143289200-143290400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:143289200-143290400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:143289200-143293400	Weak transcription	Fetal Heart	heart
33	chr4:143289200-143300000	Weak transcription	NH-A	brain
34	chr4:143289400-143290600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr4:143289400-143291400	Enhancers	NHEK	skin
36	chr4:143289600-143290600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr4:143289600-143290600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:143289800-143290200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:143289800-143290200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr4:143289800-143290200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:143289800-143290400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr4:143289800-143290400	Enhancers	HSMM	muscle
43	chr4:143289800-143290600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:143290000-143290200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr4:143290000-143290200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr4:143290000-143290200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr4:143290000-143290200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:143290000-143290600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr4:143290000-143290600	Enhancers	HSMMtube	muscle
50	chr4:143290000-143291200	Enhancers	Primary T cells fromperipheralblood	blood

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