Variant report

Variant	rs12481037
Chromosome Location	chr20:25593688-25593689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25591410..25597359-chr20:25600309..25606040,12	K562	blood:
2	chr20:25589936..25592096-chr20:25592501..25595194,2	MCF-7	breast:
3	chr20:25593129..25595979-chr20:25604532..25607057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251883	Chromatin interaction
ENSG00000170191	Chromatin interaction
ENSG00000213742	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11087526	0.87[ASN][1000 genomes]
rs11698953	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11698992	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11699872	0.93[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11700213	0.83[EUR][1000 genomes]
rs11700297	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11700338	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480853	0.83[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12625991	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1343355	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1546890	0.88[ASN][1000 genomes]
rs16987966	0.87[ASN][1000 genomes]
rs1888037	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050097	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2281212	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs3736720	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3764694	1.00[ASW][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs4813576	0.84[ASN][1000 genomes]
rs4815438	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55792313	0.82[ASN][1000 genomes]
rs57803591	0.93[ASN][1000 genomes]
rs6037190	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6050690	0.83[CHB][hapmap]
rs6115202	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6115227	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7260957	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs73109499	0.83[EUR][1000 genomes]
rs73597820	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73597824	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
3	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12481037	GINS1	cis	parietal	SCAN
rs12481037	NINL	cis	cerebellum	SCAN
rs12481037	PYGB	cis	cerebellum	SCAN
rs12481037	ABHD12	cis	lymphoblastoid	seeQTL
rs12481037	KIAA0980	cis	multi-tissue	Pritchard
rs12481037	NINL	cis	parietal	SCAN
rs12481037	ABHD12	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25580200-25603000	Weak transcription	Fetal Brain Male	brain
2	chr20:25581600-25594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr20:25581800-25594000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:25581800-25603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:25582000-25594800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:25582000-25602800	Weak transcription	Osteobl	bone
7	chr20:25583600-25594200	Weak transcription	Aorta	Aorta
8	chr20:25584400-25593800	Weak transcription	Liver	Liver
9	chr20:25585600-25595200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr20:25586000-25602600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:25586200-25602800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr20:25586400-25593800	Weak transcription	Fetal Thymus	thymus
13	chr20:25587000-25593800	Weak transcription	Fetal Muscle Leg	muscle
14	chr20:25587000-25594000	Weak transcription	HSMM	muscle
15	chr20:25587000-25603000	Weak transcription	HSMMtube	muscle
16	chr20:25587200-25594400	Weak transcription	A549	lung
17	chr20:25587400-25600400	Weak transcription	K562	blood
18	chr20:25587600-25601400	Weak transcription	Pancreas	Pancrea
19	chr20:25588000-25595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr20:25588200-25594400	Weak transcription	Primary T cells from cord blood	blood
21	chr20:25588400-25597800	Strong transcription	Dnd41	blood
22	chr20:25588400-25599200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr20:25588600-25596200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr20:25588600-25599400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr20:25588600-25599400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr20:25588600-25602800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr20:25588800-25595800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr20:25589200-25594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr20:25589200-25601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr20:25589200-25602600	Weak transcription	Right Ventricle	heart
31	chr20:25590800-25595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr20:25590800-25602600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr20:25590800-25603200	Weak transcription	Fetal Intestine Large	intestine
34	chr20:25591000-25595400	Weak transcription	Lung	lung
35	chr20:25591000-25603600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr20:25591200-25593800	Weak transcription	Thymus	Thymus
37	chr20:25591200-25594400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr20:25591200-25595400	Weak transcription	Gastric	stomach
39	chr20:25591400-25594000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr20:25591400-25602800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr20:25591600-25595200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr20:25591600-25600200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr20:25591600-25602800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr20:25591600-25603000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr20:25591600-25603200	Weak transcription	Fetal Lung	lung
46	chr20:25591800-25594000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr20:25592000-25595400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr20:25592000-25595800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr20:25592200-25593800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr20:25592200-25593800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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