Variant report

Variant	rs12594627
Chromosome Location	chr15:73986264-73986265
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73975160..73977324-chr15:73984548..73987119,2	K562	blood:
2	chr15:73956703..73958906-chr15:73984345..73986661,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103855	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11072434	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11574488	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11574495	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11574497	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11852484	0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12591553	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12593558	0.84[CEU][hapmap]
rs17185294	0.86[JPT][hapmap];0.81[LWK][hapmap]
rs17185525	0.86[JPT][hapmap]
rs2127015	0.84[EUR][1000 genomes]
rs2291011	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291013	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2509	0.86[JPT][hapmap]
rs3816661	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3935942	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61012032	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62004612	0.92[ASN][1000 genomes]
rs67257650	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs710086	0.86[JPT][hapmap]
rs8032531	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8032727	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8038465	0.92[CEU][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs8041181	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8041523	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs899981	0.82[CHB][hapmap];0.86[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12594627	CPLX3	cis	cerebellum	SCAN
rs12594627	C15orf34	cis	cerebellum	SCAN
rs12594627	LMAN1L	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73978800-73989000	Weak transcription	Fetal Kidney	kidney
2	chr15:73978800-74000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:73979400-73986800	Weak transcription	Aorta	Aorta
4	chr15:73979400-73989000	Weak transcription	Fetal Intestine Large	intestine
5	chr15:73979400-73996400	Weak transcription	A549	lung
6	chr15:73980200-73988400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:73980600-73988400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:73980600-73988400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:73981400-73988000	Weak transcription	Spleen	Spleen
10	chr15:73981600-73986400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:73981600-73987000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:73981800-73995000	Weak transcription	Pancreas	Pancrea
13	chr15:73982600-73990000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:73983600-73986400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:73984000-73986600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:73984200-73986400	Weak transcription	NH-A	brain
17	chr15:73984200-73988000	Weak transcription	Brain Substantia Nigra	brain
18	chr15:73984200-73988200	Weak transcription	HUVEC	blood vessel
19	chr15:73984200-73988800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:73984400-73986400	Weak transcription	Brain Anterior Caudate	brain
21	chr15:73984400-73986400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:73984400-73986400	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:73984400-73986400	Weak transcription	Esophagus	oesophagus
24	chr15:73984400-73986400	Weak transcription	Fetal Lung	lung
25	chr15:73984400-73986400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:73984400-73986400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:73984400-73986400	Weak transcription	Stomach Mucosa	stomach
28	chr15:73984400-73986600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:73984400-73986600	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:73984400-73987600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:73984400-73987800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:73984400-73988000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:73984400-73988000	Weak transcription	Brain Germinal Matrix	brain
34	chr15:73984400-73988600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:73984400-73989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:73984600-73986400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:73984600-73986400	Strong transcription	NHEK	skin
38	chr15:73984600-73986600	Weak transcription	Fetal Intestine Small	intestine
39	chr15:73984600-73986800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr15:73984600-73986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:73984600-73987000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:73984600-73987400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:73984600-73987800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:73984600-73988200	Weak transcription	Colonic Mucosa	Colon
45	chr15:73984600-73988400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:73984600-73988400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:73984600-73989000	Weak transcription	Hela-S3	cervix
48	chr15:73984600-73989200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:73984600-73992000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr15:73984600-73995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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