Variant report

Variant	rs6832517
Chromosome Location	chr4:99550254-99550255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99548903..99550666-chr4:99562029..99564226,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10003932	0.82[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10020677	0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs10026666	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10428298	0.87[EUR][1000 genomes]
rs11097625	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097626	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11937119	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11938081	0.84[CEU][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11941870	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11941880	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11946198	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12501391	0.87[EUR][1000 genomes]
rs12504979	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs12507537	0.87[EUR][1000 genomes]
rs12509170	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs12512885	0.96[CEU][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13435520	0.81[JPT][hapmap]
rs2178216	0.81[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2866015	0.81[CEU][hapmap]
rs3941	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]
rs4699356	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6532752	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532754	0.81[EUR][1000 genomes]
rs6819238	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6820406	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6846265	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs6852645	0.86[EUR][1000 genomes]
rs7682381	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7700024	0.87[EUR][1000 genomes]
rs7700032	0.87[EUR][1000 genomes]
rs883131	0.81[EUR][1000 genomes]
rs915879	0.81[EUR][1000 genomes]
rs9684705	0.96[CEU][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9686007	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[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
rs6832517	TSPAN5	cis	Muscle Skeletal	GTEx
rs6832517	RP11-1299A16.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99535600-99554200	Enhancers	Brain Substantia Nigra	brain
2	chr4:99544000-99552400	Weak transcription	Thymus	Thymus
3	chr4:99544400-99551200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:99546400-99554200	Enhancers	Brain Angular Gyrus	brain
5	chr4:99546600-99554000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:99546600-99560000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:99546800-99559800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:99547200-99554400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:99547800-99552400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:99547800-99552600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:99547800-99559200	Weak transcription	Stomach Mucosa	stomach
12	chr4:99548000-99550600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:99548000-99551800	Weak transcription	Right Ventricle	heart
14	chr4:99548000-99552200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:99548000-99552200	Weak transcription	Pancreas	Pancrea
16	chr4:99548000-99552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:99548000-99552400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:99548000-99552400	Weak transcription	Fetal Thymus	thymus
19	chr4:99548000-99552600	Weak transcription	Lung	lung
20	chr4:99548000-99560600	Weak transcription	Right Atrium	heart
21	chr4:99548000-99569200	Weak transcription	Gastric	stomach
22	chr4:99548000-99577000	Weak transcription	Esophagus	oesophagus
23	chr4:99548200-99551400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:99548200-99552000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:99548400-99552200	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:99548400-99552400	Weak transcription	Fetal Stomach	stomach
27	chr4:99548400-99563600	Weak transcription	HSMM	muscle
28	chr4:99548800-99551200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:99549000-99551400	Weak transcription	NHLF	lung
30	chr4:99549200-99550600	Enhancers	NHDF-Ad	bronchial
31	chr4:99549200-99550800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:99549200-99551200	Weak transcription	Fetal Brain Female	brain
33	chr4:99549200-99554000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:99549400-99550400	Weak transcription	Brain Hippocampus Middle	brain
35	chr4:99549400-99550400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:99549400-99551400	Weak transcription	Fetal Heart	heart
37	chr4:99549400-99551600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:99549400-99551600	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:99549400-99552000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:99549400-99552400	Weak transcription	Aorta	Aorta
41	chr4:99549600-99551600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:99549600-99551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:99549600-99563200	Weak transcription	HMEC	breast
44	chr4:99549800-99550400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:99549800-99550400	Weak transcription	Brain Germinal Matrix	brain
46	chr4:99549800-99550600	Weak transcription	Fetal Brain Male	brain
47	chr4:99549800-99551200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:99549800-99563600	Weak transcription	NHEK	skin
49	chr4:99550000-99551000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr4:99550000-99551200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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