Variant report

Variant	rs3941
Chromosome Location	chr4:99548182-99548183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99547655..99549957-chr4:99555367..99557808,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10003932	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10020677	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10026666	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10428298	0.89[EUR][1000 genomes]
rs11097625	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11097626	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11937119	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11938081	0.92[CEU][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941870	0.89[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11941880	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11946198	0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12501391	0.89[EUR][1000 genomes]
rs12504979	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs12507537	0.84[EUR][1000 genomes]
rs12509170	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs12512885	0.89[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2178216	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2866015	0.82[JPT][hapmap]
rs4699356	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532752	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6532754	0.82[JPT][hapmap]
rs6819238	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6820406	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6832517	0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6846265	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6852645	0.88[EUR][1000 genomes]
rs7682381	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700024	0.89[EUR][1000 genomes]
rs7700032	0.89[EUR][1000 genomes]
rs9684705	0.92[CEU][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9686007	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[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
rs3941	TSPAN5	cis	Muscle Skeletal	GTEx
rs3941	RP11-1299A16.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99535600-99554200	Enhancers	Brain Substantia Nigra	brain
2	chr4:99543400-99549400	Enhancers	Brain Hippocampus Middle	brain
3	chr4:99543400-99550000	Enhancers	Brain Cingulate Gyrus	brain
4	chr4:99543800-99548200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr4:99543800-99550000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:99544000-99550000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr4:99544000-99552400	Weak transcription	Thymus	Thymus
8	chr4:99544400-99548400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr4:99544400-99551200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:99544800-99548600	Weak transcription	Small Intestine	intestine
11	chr4:99544800-99549000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:99544800-99550000	Enhancers	NH-A	brain
13	chr4:99545000-99548200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:99545000-99549000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:99545000-99550000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:99546000-99548200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:99546000-99549200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:99546000-99549400	Enhancers	Fetal Heart	heart
19	chr4:99546200-99550000	Enhancers	Ovary	ovary
20	chr4:99546400-99549400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr4:99546400-99550000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:99546400-99554200	Enhancers	Brain Angular Gyrus	brain
23	chr4:99546600-99548400	Enhancers	HSMM	muscle
24	chr4:99546600-99548400	Flanking Active TSS	NHEK	skin
25	chr4:99546600-99549000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:99546600-99549200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:99546600-99549400	Enhancers	Colon Smooth Muscle	Colon
28	chr4:99546600-99549800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr4:99546600-99550000	Enhancers	Brain Anterior Caudate	brain
30	chr4:99546600-99554000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:99546600-99560000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:99546800-99548200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr4:99546800-99549200	Enhancers	Fetal Brain Female	brain
34	chr4:99546800-99549400	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr4:99546800-99549400	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr4:99546800-99559800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:99547000-99549200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:99547200-99548400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:99547200-99548400	Enhancers	HSMMtube	muscle
40	chr4:99547200-99549200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:99547200-99549200	Enhancers	A549	lung
42	chr4:99547200-99549400	Enhancers	Rectal Smooth Muscle	rectum
43	chr4:99547200-99554400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr4:99547400-99548400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:99547400-99548400	Flanking Active TSS	Osteobl	bone
46	chr4:99547400-99549600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:99547600-99548400	Enhancers	Fetal Muscle Leg	muscle
48	chr4:99547600-99548400	Enhancers	Left Ventricle	heart
49	chr4:99547600-99548800	Enhancers	NHDF-Ad	bronchial
50	chr4:99547600-99549000	Enhancers	NHLF	lung

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