Variant report

Variant	rs12916830
Chromosome Location	chr15:59474040-59474041
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59468439..59470202-chr15:59473986..59476480,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10519001	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs10851644	0.85[CEU][hapmap]
rs11071412	0.88[AMR][1000 genomes]
rs11631348	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11631844	0.85[ASN][1000 genomes]
rs11632420	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12898967	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903377	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12906742	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17269566	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17302219	0.83[ASN][1000 genomes]
rs2306787	1.00[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2306788	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs2899644	0.84[ASN][1000 genomes]
rs3794494	0.96[CEU][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes]
rs4775124	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4775128	0.82[AMR][1000 genomes]
rs4775130	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs56108450	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58948844	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7169503	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8041615	0.84[ASN][1000 genomes]
rs901481	0.90[AMR][1000 genomes]
rs9788755	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12916830	GCOM1	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
2	chr15:59445600-59479600	Weak transcription	Fetal Kidney	kidney
3	chr15:59451600-59474600	Weak transcription	Psoas Muscle	Psoas
4	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:59461000-59474800	Strong transcription	Liver	Liver
6	chr15:59464400-59496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:59466800-59474200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr15:59467800-59479600	Weak transcription	Brain Angular Gyrus	brain
9	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
10	chr15:59468000-59479800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:59468000-59480000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
13	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr15:59468800-59490800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr15:59468800-59492600	Strong transcription	Fetal Intestine Large	intestine
16	chr15:59469000-59482800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:59469400-59474200	Strong transcription	NHEK	skin
18	chr15:59469600-59475000	Strong transcription	HMEC	breast
19	chr15:59469800-59474800	Strong transcription	Hela-S3	cervix
20	chr15:59470000-59475800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:59470000-59482200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:59470800-59475000	Weak transcription	Lung	lung
23	chr15:59470800-59485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:59471000-59474200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:59471000-59480400	Weak transcription	Colonic Mucosa	Colon
26	chr15:59471000-59484000	Weak transcription	Esophagus	oesophagus
27	chr15:59471400-59474800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr15:59471400-59480000	Weak transcription	Left Ventricle	heart
29	chr15:59471400-59482200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:59471600-59476600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:59471800-59475200	Weak transcription	Right Ventricle	heart
32	chr15:59471800-59475800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:59471800-59479400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:59471800-59479600	Weak transcription	Gastric	stomach
35	chr15:59472000-59474600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:59472200-59474800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:59472600-59480600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:59473000-59475000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:59473000-59476200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr15:59473200-59475000	Strong transcription	Rectal Smooth Muscle	rectum
41	chr15:59473200-59475400	Strong transcription	Primary B cells from cord blood	blood
42	chr15:59473200-59477600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:59473400-59474400	Weak transcription	Fetal Stomach	stomach
44	chr15:59473400-59474600	Weak transcription	Aorta	Aorta
45	chr15:59473400-59474600	Weak transcription	Pancreas	Pancrea
46	chr15:59473400-59475000	Weak transcription	Ovary	ovary
47	chr15:59473400-59475400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:59473400-59475400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
49	chr15:59473400-59482200	Weak transcription	Spleen	Spleen
50	chr15:59473600-59474200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--

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