Variant report

Variant	rs6820406
Chromosome Location	chr4:99552178-99552179
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99551429..99553596-chr4:99563119..99565613,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10003932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020677	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10026666	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938081	0.80[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11941870	0.86[JPT][hapmap]
rs11941880	0.88[JPT][hapmap]
rs11946198	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs2178216	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2866015	0.84[CEU][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs3941	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4699356	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs6532754	0.81[CEU][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs6819238	0.84[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs6832517	0.82[CEU][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6846265	0.82[JPT][hapmap]
rs7682381	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9684705	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs9686007	0.82[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
rs6820406	TSPAN5	cis	Muscle Skeletal	GTEx
rs6820406	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	chr4:99546400-99554200	Enhancers	Brain Angular Gyrus	brain
4	chr4:99546600-99554000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:99546600-99560000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:99546800-99559800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:99547200-99554400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:99547800-99552400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:99547800-99552600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:99547800-99559200	Weak transcription	Stomach Mucosa	stomach
11	chr4:99548000-99552200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:99548000-99552200	Weak transcription	Pancreas	Pancrea
13	chr4:99548000-99552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:99548000-99552400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:99548000-99552400	Weak transcription	Fetal Thymus	thymus
16	chr4:99548000-99552600	Weak transcription	Lung	lung
17	chr4:99548000-99560600	Weak transcription	Right Atrium	heart
18	chr4:99548000-99569200	Weak transcription	Gastric	stomach
19	chr4:99548000-99577000	Weak transcription	Esophagus	oesophagus
20	chr4:99548400-99552200	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:99548400-99552400	Weak transcription	Fetal Stomach	stomach
22	chr4:99548400-99563600	Weak transcription	HSMM	muscle
23	chr4:99549200-99554000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:99549400-99552400	Weak transcription	Aorta	Aorta
25	chr4:99549600-99563200	Weak transcription	HMEC	breast
26	chr4:99549800-99563600	Weak transcription	NHEK	skin
27	chr4:99550000-99553200	Weak transcription	NH-A	brain
28	chr4:99550000-99553800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:99550000-99563600	Weak transcription	HUVEC	blood vessel
30	chr4:99550400-99554200	Enhancers	Brain Hippocampus Middle	brain
31	chr4:99550400-99554800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:99550600-99555000	Enhancers	Fetal Brain Male	brain
33	chr4:99550800-99553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:99551000-99554600	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:99551200-99552600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:99551200-99553000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr4:99551200-99553800	Enhancers	Fetal Brain Female	brain
38	chr4:99551200-99554200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr4:99551200-99554400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr4:99551400-99552400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:99551400-99553200	Enhancers	NHLF	lung
42	chr4:99551400-99553600	Enhancers	Fetal Heart	heart
43	chr4:99551400-99554200	Enhancers	NHDF-Ad	bronchial
44	chr4:99551400-99554400	Enhancers	Brain Anterior Caudate	brain
45	chr4:99551400-99554400	Enhancers	Ovary	ovary
46	chr4:99551600-99552200	Enhancers	Colon Smooth Muscle	Colon
47	chr4:99551600-99553600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:99551600-99554000	Enhancers	Osteobl	bone
49	chr4:99551600-99555000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:99551800-99552400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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