Variant report

Variant	rs11938081
Chromosome Location	chr4:99547094-99547095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10003932	0.80[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10020677	0.80[ASN][1000 genomes]
rs10026666	0.80[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10428298	0.89[EUR][1000 genomes]
rs11097625	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097626	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11937119	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11941870	0.88[CEU][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11941880	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11946198	0.80[CEU][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12501391	0.90[EUR][1000 genomes]
rs12504979	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12507537	0.85[EUR][1000 genomes]
rs12509170	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12512885	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178216	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2866015	0.85[JPT][hapmap]
rs3941	0.92[CEU][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699356	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532752	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532754	0.85[JPT][hapmap]
rs6819238	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6820406	0.80[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6832517	0.84[CEU][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6846265	0.85[JPT][hapmap]
rs6848644	0.86[ASN][1000 genomes]
rs6852645	0.88[EUR][1000 genomes]
rs7682381	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7700024	0.89[EUR][1000 genomes]
rs7700032	0.89[EUR][1000 genomes]
rs9684705	0.82[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9686007	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594940	chr4:99542475-99573350	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11938081	RP11-1299A16.3	cis	Muscle Skeletal	GTEx
rs11938081	TSPAN5	cis	Muscle Skeletal	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99535600-99554200	Enhancers	Brain Substantia Nigra	brain
2	chr4:99539000-99547200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:99539200-99547200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:99539200-99547200	Weak transcription	Right Atrium	heart
5	chr4:99539200-99547600	Weak transcription	Gastric	stomach
6	chr4:99539200-99547600	Weak transcription	Left Ventricle	heart
7	chr4:99539200-99547600	Weak transcription	Right Ventricle	heart
8	chr4:99539200-99547800	Weak transcription	Fetal Stomach	stomach
9	chr4:99540000-99547400	Weak transcription	Fetal Lung	lung
10	chr4:99542000-99547200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:99542000-99547200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:99542000-99547200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:99542200-99547600	Weak transcription	Fetal Brain Male	brain
14	chr4:99542400-99547200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:99543200-99547200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:99543400-99547200	Enhancers	NHDF-Ad	bronchial
17	chr4:99543400-99547200	Enhancers	NHLF	lung
18	chr4:99543400-99549400	Enhancers	Brain Hippocampus Middle	brain
19	chr4:99543400-99550000	Enhancers	Brain Cingulate Gyrus	brain
20	chr4:99543600-99547200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:99543800-99548200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr4:99543800-99550000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:99544000-99550000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr4:99544000-99552400	Weak transcription	Thymus	Thymus
25	chr4:99544200-99547200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr4:99544200-99547400	Enhancers	Osteobl	bone
27	chr4:99544400-99547800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:99544400-99548400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr4:99544400-99551200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:99544600-99547200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:99544600-99547200	Weak transcription	Primary B cells from cord blood	blood
32	chr4:99544600-99547800	Weak transcription	Brain Germinal Matrix	brain
33	chr4:99544800-99547400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:99544800-99548600	Weak transcription	Small Intestine	intestine
35	chr4:99544800-99549000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:99544800-99550000	Enhancers	NH-A	brain
37	chr4:99545000-99548200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:99545000-99549000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr4:99545000-99550000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:99545200-99547200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:99545200-99547400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:99545800-99547800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:99545800-99548000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:99546000-99547200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:99546000-99548200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:99546000-99549200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:99546000-99549400	Enhancers	Fetal Heart	heart
48	chr4:99546200-99547600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:99546200-99550000	Enhancers	Ovary	ovary
50	chr4:99546400-99547600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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