Variant report

Variant	rs11143589
Chromosome Location	chr9:71356019-71356020
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11143572	0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11789971	0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs12686355	0.82[ASW][hapmap]
rs13296679	0.95[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs34414551	0.88[ASN][1000 genomes]
rs35213801	0.86[ASN][1000 genomes]
rs4745236	0.83[YRI][hapmap]
rs7032100	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7043892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7044032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7044045	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7044422	0.81[LWK][hapmap]
rs7866673	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026962	chr9:71130848-71357605	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv893415	chr9:71347988-71364351	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11143589	MAMDC2	cis	parietal	SCAN
rs11143589	GALNT4	trans	parietal	SCAN
rs11143589	PGM5	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71343400-71363000	Weak transcription	GM12878-XiMat	blood
2	chr9:71343800-71357200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr9:71347400-71357800	Weak transcription	Primary B cells from cord blood	blood
4	chr9:71348200-71359000	Weak transcription	Lung	lung
5	chr9:71350000-71356600	Weak transcription	Aorta	Aorta
6	chr9:71351000-71370600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:71351200-71360000	Weak transcription	Gastric	stomach
8	chr9:71352400-71365800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:71353400-71356600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:71353800-71356200	Weak transcription	Colonic Mucosa	Colon
11	chr9:71354000-71356400	Weak transcription	Small Intestine	intestine
12	chr9:71354400-71356400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:71354400-71356800	Enhancers	Left Ventricle	heart
14	chr9:71354400-71356800	Enhancers	Pancreas	Pancrea
15	chr9:71354600-71357200	Enhancers	K562	blood
16	chr9:71354800-71356200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr9:71354800-71361600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:71355000-71356200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:71355000-71356800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:71355000-71359000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:71355000-71359400	Weak transcription	Right Ventricle	heart
22	chr9:71355000-71360000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:71355000-71362000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr9:71355000-71364400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:71355000-71365400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:71355200-71356200	Weak transcription	Right Atrium	heart
27	chr9:71355200-71356200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:71355200-71357600	Weak transcription	Placenta	Placenta
29	chr9:71355400-71357000	Enhancers	Fetal Heart	heart
30	chr9:71355400-71358600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr9:71355400-71361600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:71355600-71356200	Weak transcription	Stomach Mucosa	stomach
33	chr9:71355600-71357600	Enhancers	Fetal Intestine Large	intestine
34	chr9:71355600-71361600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr9:71355600-71364200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:71355800-71356200	Weak transcription	Fetal Intestine Small	intestine
37	chr9:71355800-71356800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr9:71356000-71356400	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr9:71356000-71356800	Enhancers	HepG2	liver
40	chr9:71356000-71358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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