Variant report

Variant	rs12512885
Chromosome Location	chr4:99541753-99541754
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	chr4:99540036..99541915-chr4:99662055..99663703,2	K562	blood:
2	chr4:99537720..99540148-chr4:99541688..99544622,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10428298	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11097625	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097626	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11937119	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11938081	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11941870	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11941880	0.96[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11946198	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12501391	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12504979	0.84[ASN][1000 genomes]
rs12507537	0.91[EUR][1000 genomes]
rs12509170	0.84[ASN][1000 genomes]
rs2178216	0.92[ASN][1000 genomes]
rs2866015	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs3941	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]
rs4699356	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532752	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6532753	0.80[EUR][1000 genomes]
rs6532754	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs6819238	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6832517	0.96[CEU][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6846265	0.85[CEU][hapmap];0.83[ASN][1000 genomes]
rs6848644	0.87[ASN][1000 genomes]
rs6852645	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7682381	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7700024	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7700032	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883131	0.85[EUR][1000 genomes]
rs915879	0.85[EUR][1000 genomes]
rs9684705	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9686007	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12512885	RP11-1299A16.3	cis	Muscle Skeletal	GTEx
rs12512885	TSPAN5	cis	Muscle Skeletal	GTEx

Chromatin state (count:74 , 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	chr4:99529600-99542400	Enhancers	Brain Cingulate Gyrus	brain
3	chr4:99529600-99543200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:99531000-99544200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:99532600-99545400	Weak transcription	HMEC	breast
6	chr4:99534400-99543200	Weak transcription	Thymus	Thymus
7	chr4:99535400-99544200	Weak transcription	NHEK	skin
8	chr4:99535600-99554200	Enhancers	Brain Substantia Nigra	brain
9	chr4:99536200-99545800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:99536800-99541800	Enhancers	Fetal Brain Female	brain
11	chr4:99536800-99542400	Enhancers	Brain Angular Gyrus	brain
12	chr4:99537600-99544800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:99538000-99542200	Enhancers	Fetal Brain Male	brain
14	chr4:99538200-99542600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:99538400-99542000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:99538400-99542200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:99538400-99543800	Enhancers	Brain Anterior Caudate	brain
18	chr4:99539000-99546400	Weak transcription	Fetal Thymus	thymus
19	chr4:99539000-99547200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:99539200-99543400	Weak transcription	NHDF-Ad	bronchial
21	chr4:99539200-99544200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:99539200-99544200	Weak transcription	Osteobl	bone
23	chr4:99539200-99545400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:99539200-99546000	Weak transcription	Fetal Heart	heart
25	chr4:99539200-99546600	Weak transcription	HSMM	muscle
26	chr4:99539200-99547200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:99539200-99547200	Weak transcription	Right Atrium	heart
28	chr4:99539200-99547600	Weak transcription	Gastric	stomach
29	chr4:99539200-99547600	Weak transcription	Left Ventricle	heart
30	chr4:99539200-99547600	Weak transcription	Right Ventricle	heart
31	chr4:99539200-99547800	Weak transcription	Fetal Stomach	stomach
32	chr4:99539800-99542400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:99539800-99542400	Enhancers	Brain Germinal Matrix	brain
34	chr4:99540000-99542000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:99540000-99547400	Weak transcription	Fetal Lung	lung
36	chr4:99540400-99542600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:99540400-99543600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:99540600-99542000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:99540600-99542200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:99540800-99542200	Enhancers	Brain Hippocampus Middle	brain
41	chr4:99541000-99541800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:99541000-99541800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:99541000-99541800	Strong transcription	NHLF	lung
44	chr4:99541000-99542000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr4:99541000-99542000	Enhancers	Primary T cells fromperipheralblood	blood
46	chr4:99541000-99542200	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr4:99541000-99542400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:99541000-99543200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:99541000-99544000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr4:99541200-99541800	Enhancers	Primary T helper cells PMA-I stimulated	--

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