Variant report

Variant	rs12185108
Chromosome Location	chr15:73892952-73892953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73891083..73895912-chr15:73975299..73977983,6	MCF-7	breast:
2	chr15:73890210..73895158-chr15:73907012..73911430,4	MCF-7	breast:
3	chr15:73887376..73889104-chr15:73891545..73893997,2	MCF-7	breast:
4	chr15:73892279..73895385-chr15:73924684..73929029,4	MCF-7	breast:
5	chr15:73892805..73894766-chr15:73916843..73918631,2	MCF-7	breast:
6	chr15:73881398..73883400-chr15:73891202..73894116,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156642	Chromatin interaction
ENSG00000103855	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10851863	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072428	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072429	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072430	0.80[JPT][hapmap]
rs11072431	0.80[JPT][hapmap]
rs12148532	0.86[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12148719	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442903	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12593246	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383616	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1481088	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1481089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16958079	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743500	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4470111	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4558379	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495069	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495075	0.80[JPT][hapmap]
rs6495076	0.82[JPT][hapmap]
rs7169374	0.88[ASN][1000 genomes]
rs7176637	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023823	0.87[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8028089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037836	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs922687	0.90[ASN][1000 genomes]
rs9920359	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12185108	ARIH1	cis	cerebellum	SCAN
rs12185108	FEZ1	trans	lymphoblastoid	seeQTL
rs12185108	LMAN1L	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73847400-73893200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:73880000-73894600	Weak transcription	Fetal Thymus	thymus
3	chr15:73880200-73894000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:73881200-73893800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:73881400-73894000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:73881400-73894400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:73882000-73893800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:73882200-73895000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:73882800-73893200	Weak transcription	Liver	Liver
10	chr15:73882800-73893200	Weak transcription	Colonic Mucosa	Colon
11	chr15:73882800-73894200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:73884400-73893200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:73884400-73894000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:73884600-73893400	Weak transcription	Fetal Kidney	kidney
15	chr15:73884600-73893800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:73884600-73894000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:73884600-73894200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:73884600-73894400	Weak transcription	Thymus	Thymus
19	chr15:73884800-73894000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:73885600-73894800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr15:73885600-73895600	Enhancers	Brain Cingulate Gyrus	brain
22	chr15:73885800-73895400	Enhancers	Right Atrium	heart
23	chr15:73885800-73895400	Enhancers	Right Ventricle	heart
24	chr15:73885800-73895800	Enhancers	Brain Anterior Caudate	brain
25	chr15:73885800-73895800	Enhancers	Psoas Muscle	Psoas
26	chr15:73885800-73896200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr15:73885800-73896200	Enhancers	Colon Smooth Muscle	Colon
28	chr15:73886200-73893400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:73886400-73893400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr15:73886400-73895600	Enhancers	Small Intestine	intestine
31	chr15:73886800-73893200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr15:73886800-73893200	Weak transcription	Fetal Brain Female	brain
33	chr15:73886800-73893800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr15:73886800-73895400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:73887000-73894400	Weak transcription	Primary T cells from cord blood	blood
36	chr15:73887800-73893800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:73888000-73895200	Enhancers	Ovary	ovary
38	chr15:73888200-73894400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:73888200-73895600	Enhancers	HMEC	breast
40	chr15:73888200-73895600	Enhancers	Osteobl	bone
41	chr15:73888400-73894000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr15:73888400-73896400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:73888600-73895200	Enhancers	Fetal Muscle Leg	muscle
44	chr15:73888800-73893400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:73888800-73893600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:73889200-73893800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:73889600-73893200	Weak transcription	Placenta	Placenta
48	chr15:73889600-73895800	Enhancers	Left Ventricle	heart
49	chr15:73889800-73893200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:73889800-73894000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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