Variant report

Variant	rs2866015
Chromosome Location	chr4:99539498-99539499
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99494665..99495526-chr4:99539142..99539720,2	MCF-7	breast:
2	chr4:99537720..99540148-chr4:99541688..99544622,2	K562	blood:
3	chr4:99426512..99427492-chr4:99538749..99539662,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10003932	0.84[CEU][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs10026666	0.84[CEU][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs11097625	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11097626	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11937119	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11938081	0.85[JPT][hapmap]
rs11941870	0.80[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11941880	0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11946198	0.91[ASW][hapmap];0.81[CEU][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12512885	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs2178216	0.85[JPT][hapmap]
rs3941	0.82[JPT][hapmap]
rs4699356	0.91[ASW][hapmap];0.81[CEU][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6532752	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6532753	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6819238	0.91[ASW][hapmap];0.81[CEU][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6820406	0.84[CEU][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs6832517	0.81[CEU][hapmap]
rs6846265	0.87[JPT][hapmap]
rs883131	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs915879	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9684705	0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9686007	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2866015	RP11-1299A16.3	cis	Muscle Skeletal	GTEx
rs2866015	TSPAN5	cis	Muscle Skeletal	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99523000-99545000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:99527200-99541000	Weak transcription	NHLF	lung
3	chr4:99529400-99539800	Enhancers	Brain Hippocampus Middle	brain
4	chr4:99529600-99542400	Enhancers	Brain Cingulate Gyrus	brain
5	chr4:99529600-99543200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:99530000-99540600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:99531000-99544200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:99531200-99541400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:99532600-99545400	Weak transcription	HMEC	breast
10	chr4:99534000-99541400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:99534200-99541400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:99534400-99541200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:99534400-99543200	Weak transcription	Thymus	Thymus
14	chr4:99534600-99541000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:99535000-99541400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:99535000-99541600	Enhancers	Ovary	ovary
17	chr4:99535200-99541200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:99535400-99540000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:99535400-99541000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:99535400-99544200	Weak transcription	NHEK	skin
21	chr4:99535600-99539800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:99535600-99541200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:99535600-99554200	Enhancers	Brain Substantia Nigra	brain
24	chr4:99535800-99539800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:99536200-99545800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:99536400-99541000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:99536800-99541800	Enhancers	Fetal Brain Female	brain
28	chr4:99536800-99542400	Enhancers	Brain Angular Gyrus	brain
29	chr4:99537600-99544800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:99538000-99542200	Enhancers	Fetal Brain Male	brain
31	chr4:99538200-99541200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr4:99538200-99542600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:99538400-99539600	Enhancers	HUVEC	blood vessel
34	chr4:99538400-99541000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:99538400-99542000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:99538400-99542200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:99538400-99543800	Enhancers	Brain Anterior Caudate	brain
38	chr4:99539000-99541200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:99539000-99541200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:99539000-99541400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:99539000-99541400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:99539000-99541400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:99539000-99546400	Weak transcription	Fetal Thymus	thymus
44	chr4:99539000-99547200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:99539200-99540000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:99539200-99540200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:99539200-99540400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:99539200-99540400	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:99539200-99540400	Weak transcription	Fetal Muscle Leg	muscle
50	chr4:99539200-99541000	Weak transcription	Primary T cells fromperipheralblood	blood

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