Variant report

Variant	rs10428298
Chromosome Location	chr4:99531993-99531994
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	chr12:67709812..67710332-chr4:99531489..99532009,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11097625	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11097626	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11937119	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11938081	0.89[EUR][1000 genomes]
rs11941870	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11941880	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11946198	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12501391	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12507537	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12509046	0.86[ASN][1000 genomes]
rs12512885	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28531755	0.84[ASN][1000 genomes]
rs3941	0.89[EUR][1000 genomes]
rs4699356	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4699660	0.84[ASN][1000 genomes]
rs4699661	0.84[ASN][1000 genomes]
rs4699662	0.83[ASN][1000 genomes]
rs6532752	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6819238	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6832517	0.87[EUR][1000 genomes]
rs6846265	0.99[ASN][1000 genomes]
rs6852645	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682381	0.89[EUR][1000 genomes]
rs7700024	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700032	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9684705	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9686007	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10428298	TSPAN5	cis	Muscle Skeletal	GTEx
rs10428298	RP11-1299A16.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99522200-99532200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr4:99523000-99545000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:99523600-99532200	Weak transcription	HMEC	breast
4	chr4:99524000-99535400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:99525400-99533200	Weak transcription	Fetal Lung	lung
6	chr4:99527200-99532200	Weak transcription	Gastric	stomach
7	chr4:99527200-99534400	Weak transcription	Osteobl	bone
8	chr4:99527200-99541000	Weak transcription	NHLF	lung
9	chr4:99527400-99532000	Weak transcription	NHDF-Ad	bronchial
10	chr4:99528000-99534600	Enhancers	Fetal Thymus	thymus
11	chr4:99529200-99532200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:99529200-99533000	Enhancers	Brain Germinal Matrix	brain
13	chr4:99529200-99533000	Enhancers	Fetal Brain Female	brain
14	chr4:99529200-99535400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:99529200-99535400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:99529200-99537800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr4:99529400-99535000	Enhancers	Brain Substantia Nigra	brain
18	chr4:99529400-99536200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:99529400-99536400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:99529400-99536400	Enhancers	Brain Angular Gyrus	brain
21	chr4:99529400-99536600	Enhancers	Fetal Brain Male	brain
22	chr4:99529400-99539800	Enhancers	Brain Hippocampus Middle	brain
23	chr4:99529600-99532000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr4:99529600-99533600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:99529600-99535600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:99529600-99535800	Enhancers	Brain Anterior Caudate	brain
27	chr4:99529600-99542400	Enhancers	Brain Cingulate Gyrus	brain
28	chr4:99529600-99543200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr4:99529800-99536400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:99529800-99538600	Weak transcription	Lung	lung
31	chr4:99530000-99533800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:99530000-99535400	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:99530000-99540600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:99530200-99533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:99530200-99533800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:99530200-99534000	Enhancers	Ovary	ovary
37	chr4:99530400-99532200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr4:99530400-99532400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:99530400-99534000	Weak transcription	Primary T cells from cord blood	blood
40	chr4:99530400-99537400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:99530400-99538400	Weak transcription	HUVEC	blood vessel
42	chr4:99530600-99532000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:99530600-99535600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:99530800-99533200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:99530800-99534000	Enhancers	H9 Cell Line	embryonic stem cell
46	chr4:99530800-99534000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:99530800-99537400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr4:99531000-99532600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:99531000-99534600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr4:99531000-99538000	Enhancers	NH-A	brain

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