Variant report

Variant	rs12444747
Chromosome Location	chr16:81074904-81074905
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81036155..81041262-chr16:81074086..81079875,7	K562	blood:
2	chr16:81073990..81076535-chr16:81110612..81112776,2	MCF-7	breast:
3	chr16:81074762..81077123-chr16:81078708..81080321,2	K562	blood:
4	chr16:81068207..81071925-chr16:81073357..81079831,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166454	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000260213	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1035541	0.88[EUR][1000 genomes]
rs10459871	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs10459872	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1048194	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050364	0.80[EUR][1000 genomes]
rs10514512	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs10514513	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs10514514	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs10514515	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs11537	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs11866124	0.80[CEU][hapmap]
rs12443549	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12444137	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12444969	0.84[EUR][1000 genomes]
rs12444974	0.80[CEU][hapmap]
rs12445303	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs12448806	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12456	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12598621	0.80[EUR][1000 genomes]
rs13185	0.80[CEU][hapmap]
rs1414	0.89[CEU][hapmap]
rs1563072	0.80[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563075	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs1563077	0.80[EUR][1000 genomes]
rs16954505	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs16954513	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954572	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs16954582	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2278022	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2278024	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2287995	0.87[EUR][1000 genomes]
rs2316730	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317087	0.84[EUR][1000 genomes]
rs2549891	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2549896	0.89[CEU][hapmap]
rs2602402	0.89[CEU][hapmap]
rs2602407	0.89[CEU][hapmap]
rs28391685	0.80[EUR][1000 genomes]
rs28613188	0.80[EUR][1000 genomes]
rs28672349	0.80[EUR][1000 genomes]
rs2970076	0.89[CEU][hapmap]
rs2970077	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4306521	0.80[EUR][1000 genomes]
rs4324141	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs4324142	0.80[EUR][1000 genomes]
rs4324143	0.80[EUR][1000 genomes]
rs4889225	0.89[CEU][hapmap]
rs4889227	0.80[EUR][1000 genomes]
rs4889231	0.80[EUR][1000 genomes]
rs4889233	0.80[CEU][hapmap]
rs55939311	0.82[EUR][1000 genomes]
rs56032321	0.80[EUR][1000 genomes]
rs56119129	0.80[EUR][1000 genomes]
rs56166222	0.82[EUR][1000 genomes]
rs56198248	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56286107	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375210	1.00[ASN][1000 genomes]
rs56395947	0.80[EUR][1000 genomes]
rs57606521	1.00[ASN][1000 genomes]
rs58144189	0.89[EUR][1000 genomes]
rs59177227	0.80[EUR][1000 genomes]
rs59685942	0.80[EUR][1000 genomes]
rs61082942	0.80[EUR][1000 genomes]
rs6420421	0.80[CEU][hapmap]
rs7188508	0.80[EUR][1000 genomes]
rs7204040	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7206814	0.89[CEU][hapmap]
rs73597252	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754429	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs8043855	0.89[CEU][hapmap]
rs804885	0.89[CEU][hapmap]
rs804895	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs804897	0.85[EUR][1000 genomes]
rs804902	0.89[CEU][hapmap]
rs8052490	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs8056972	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs8059692	0.80[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177851	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177876	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177940	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs8177942	0.82[EUR][1000 genomes]
rs8177943	0.80[EUR][1000 genomes]
rs8177948	0.80[EUR][1000 genomes]
rs8177950	0.80[EUR][1000 genomes]
rs8177957	0.89[CEU][hapmap]
rs8177959	0.89[CEU][hapmap]
rs874437	0.86[EUR][1000 genomes]
rs935942	0.89[CEU][hapmap]
rs9806918	0.84[EUR][1000 genomes]
rs9923732	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs9925940	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9925943	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9926174	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9929586	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9933184	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9938965	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv995083	chr16:81050917-81076406	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12444747	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs12444747	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs12444747	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs12444747	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs12444747	GCSH	cis	Muscle Skeletal	GTEx
rs12444747	ATMIN	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81070600-81075800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:81070800-81081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:81071000-81075200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr16:81071000-81075200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:81071000-81075400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr16:81071000-81075400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr16:81071000-81075800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr16:81071000-81076400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr16:81071000-81079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr16:81071200-81075000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr16:81071200-81075000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr16:81071200-81075000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:81071200-81075000	Enhancers	Brain Cingulate Gyrus	brain
14	chr16:81071200-81075000	Weak transcription	Brain Germinal Matrix	brain
15	chr16:81071200-81075000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr16:81071200-81075000	Weak transcription	Fetal Kidney	kidney
17	chr16:81071200-81075000	Weak transcription	Fetal Lung	lung
18	chr16:81071200-81075000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr16:81071200-81075000	Weak transcription	Right Ventricle	heart
20	chr16:81071200-81075000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr16:81071200-81075000	Weak transcription	HSMMtube	muscle
22	chr16:81071200-81075000	Weak transcription	NHLF	lung
23	chr16:81071200-81075000	Weak transcription	Osteobl	bone
24	chr16:81071200-81075200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr16:81071200-81075200	Weak transcription	Aorta	Aorta
26	chr16:81071200-81075200	Weak transcription	Colonic Mucosa	Colon
27	chr16:81071200-81075200	Weak transcription	NHDF-Ad	bronchial
28	chr16:81071200-81075400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr16:81071200-81080400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr16:81071200-81080400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr16:81071200-81080600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr16:81071200-81082000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr16:81071200-81082400	Weak transcription	Stomach Mucosa	stomach
34	chr16:81071400-81075000	Weak transcription	Adipose Nuclei	Adipose
35	chr16:81071400-81079400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr16:81071400-81079600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr16:81071400-81079800	Strong transcription	Fetal Intestine Large	intestine
38	chr16:81071600-81080600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr16:81071800-81081800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr16:81072000-81079400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr16:81072200-81079400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr16:81072400-81075200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr16:81072400-81075200	Weak transcription	Colon Smooth Muscle	Colon
44	chr16:81072400-81075200	Weak transcription	Psoas Muscle	Psoas
45	chr16:81072400-81079800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr16:81072600-81075000	Weak transcription	Pancreas	Pancrea
47	chr16:81072600-81075200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:81072600-81075800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr16:81072800-81075000	Weak transcription	Esophagus	oesophagus
50	chr16:81072800-81075000	Weak transcription	Fetal Intestine Small	intestine

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