Variant report

Variant	rs11175217
Chromosome Location	chr12:64359018-64359019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64356528..64360671-chr12:64362501..64365112,4	MCF-7	breast:
2	chr12:64350699..64353399-chr12:64355633..64359154,3	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11175227	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1350138	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1350140	0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs1947504	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1962538	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054150	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741607	0.81[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs4516056	0.94[JPT][hapmap]
rs4604983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6581515	0.82[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs7300256	0.86[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7300468	0.82[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs7313754	0.82[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs7957913	0.82[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap]
rs9668855	0.81[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv559201	chr12:64333212-64366408	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11175217	DPY19L2	cis	cerebellum	SCAN
rs11175217	C12orf66	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64312400-64385000	Weak transcription	Aorta	Aorta
2	chr12:64328800-64360800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:64340000-64360200	Weak transcription	NHEK	skin
4	chr12:64344200-64361000	Weak transcription	HMEC	breast
5	chr12:64344600-64359800	Weak transcription	Small Intestine	intestine
6	chr12:64344600-64363800	Weak transcription	Fetal Intestine Small	intestine
7	chr12:64345400-64363800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:64346000-64365400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:64347000-64361400	Weak transcription	Brain Anterior Caudate	brain
10	chr12:64350400-64361000	Weak transcription	HSMM	muscle
11	chr12:64352600-64361400	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:64354600-64361000	Weak transcription	Fetal Brain Female	brain
13	chr12:64355200-64361000	Weak transcription	Right Atrium	heart
14	chr12:64355200-64361600	Weak transcription	Fetal Brain Male	brain
15	chr12:64355400-64359800	Weak transcription	NHLF	lung
16	chr12:64355400-64360200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:64355400-64361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:64355400-64361200	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:64355400-64362200	Weak transcription	Pancreas	Pancrea
20	chr12:64355600-64360400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:64355600-64363800	Weak transcription	Adipose Nuclei	Adipose
22	chr12:64355800-64361000	Weak transcription	Ovary	ovary
23	chr12:64356400-64359600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:64357200-64362400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:64357800-64359200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:64358400-64359400	Weak transcription	Osteobl	bone
27	chr12:64358400-64359800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:64358400-64361400	Weak transcription	HSMMtube	muscle
29	chr12:64358400-64362400	Weak transcription	Psoas Muscle	Psoas
30	chr12:64358600-64360200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:64358600-64360600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:64358600-64363000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr12:64358800-64360000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:64358800-64360000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:64358800-64360400	Weak transcription	A549	lung
36	chr12:64358800-64361000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:64358800-64362200	Weak transcription	Brain Substantia Nigra	brain
38	chr12:64358800-64363200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:64359000-64359400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:64359000-64359600	Weak transcription	NHDF-Ad	bronchial
41	chr12:64359000-64360000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:64359000-64360400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:64359000-64361200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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