Variant report

Variant	rs11071412
Chromosome Location	chr15:59480141-59480142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1032180	0.83[ASN][1000 genomes]
rs10519001	0.89[CEU][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10851644	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs11630106	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11631348	0.83[EUR][1000 genomes]
rs11632420	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12898967	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12903377	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906742	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916830	0.88[AMR][1000 genomes]
rs17269566	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2129426	0.80[ASN][1000 genomes]
rs2306787	0.96[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs2306788	0.96[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2306789	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794494	1.00[CEU][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794499	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3794500	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4775124	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4775130	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs56108450	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58948844	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7162863	0.83[ASN][1000 genomes]
rs7169503	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs901481	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9788755	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11071412	GCOM1	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
2	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:59464400-59496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
5	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
6	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr15:59468800-59490800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr15:59468800-59492600	Strong transcription	Fetal Intestine Large	intestine
9	chr15:59469000-59482800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:59470000-59482200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:59470800-59485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:59471000-59480400	Weak transcription	Colonic Mucosa	Colon
13	chr15:59471000-59484000	Weak transcription	Esophagus	oesophagus
14	chr15:59471400-59482200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:59472600-59480600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:59473400-59482200	Weak transcription	Spleen	Spleen
17	chr15:59474000-59483400	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:59474400-59482400	Weak transcription	HepG2	liver
19	chr15:59474400-59483800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:59474400-59484600	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:59475000-59483000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:59475000-59483000	Strong transcription	NHEK	skin
23	chr15:59475200-59480600	Strong transcription	HSMM	muscle
24	chr15:59475200-59486800	Weak transcription	Pancreas	Pancrea
25	chr15:59475200-59503200	Strong transcription	Liver	Liver
26	chr15:59475400-59485200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:59475800-59483800	Strong transcription	Hela-S3	cervix
28	chr15:59475800-59498200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr15:59475800-59517800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:59476000-59488000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:59476200-59490600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr15:59476400-59482800	Strong transcription	NHDF-Ad	bronchial
33	chr15:59476600-59482600	Strong transcription	HMEC	breast
34	chr15:59476800-59486400	Weak transcription	Right Ventricle	heart
35	chr15:59477000-59498000	Strong transcription	GM12878-XiMat	blood
36	chr15:59477400-59481600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:59477600-59485400	Weak transcription	Small Intestine	intestine
38	chr15:59477800-59486800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:59478000-59483000	Strong transcription	HUVEC	blood vessel
40	chr15:59478200-59480600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:59478800-59481200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:59478800-59481600	Weak transcription	HSMMtube	muscle
43	chr15:59478800-59483200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:59478800-59486800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:59479200-59482600	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr15:59479200-59483200	Strong transcription	Osteobl	bone
47	chr15:59479400-59480800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:59479400-59482000	Strong transcription	Placenta	Placenta
49	chr15:59479400-59482400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr15:59479400-59483000	Strong transcription	Adipose Nuclei	Adipose

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