Variant report

Variant	rs1189442
Chromosome Location	chr13:95709395-95709396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:95709169-95709400	K562	blood:	n/a	n/a

Variant related genes	Relation type
ABCC4	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1151471	0.86[JPT][hapmap]
rs1189334	0.84[ASN][1000 genomes]
rs1189433	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1189435	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs1189436	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs1189437	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs1189439	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs1189441	0.96[ASN][1000 genomes]
rs1189443	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1189444	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1189445	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1189446	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1189449	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1189451	0.87[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1189452	0.87[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1189453	0.82[ASN][1000 genomes]
rs1189456	0.85[ASN][1000 genomes]
rs1189461	0.81[CHD][hapmap];0.86[ASN][1000 genomes]
rs1189462	0.81[CHD][hapmap];0.86[ASN][1000 genomes]
rs1189463	0.80[ASN][1000 genomes]
rs1189464	0.86[ASN][1000 genomes]
rs1189466	0.81[CHD][hapmap];0.86[ASN][1000 genomes]
rs1189467	0.84[ASN][1000 genomes]
rs1211485	0.86[ASN][1000 genomes]
rs1612388	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1629441	0.93[ASN][1000 genomes]
rs1630901	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1678339	0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs1678365	0.81[CHD][hapmap];0.86[ASN][1000 genomes]
rs1678387	0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs1678395	0.86[CHB][hapmap]
rs1678409	0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1729745	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1729747	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1729752	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1751031	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1751033	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1751034	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1751036	0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1751037	0.81[CHD][hapmap];0.86[ASN][1000 genomes]
rs1751042	0.84[ASN][1000 genomes]
rs1751043	0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs2619312	0.87[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2766475	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2950957	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs4148540	0.92[CHB][hapmap];0.87[CHD][hapmap]
rs5016378	0.87[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs7331488	0.92[CHB][hapmap];0.81[CHD][hapmap]
rs7338853	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs931111	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9524790	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832688	chr13:95633193-95780198	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv525194	chr13:95672950-95737192	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1189442	NSUN7	trans	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95655600-95722600	Weak transcription	Gastric	stomach
2	chr13:95668600-95712000	Weak transcription	NHDF-Ad	bronchial
3	chr13:95669400-95723200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr13:95669600-95744000	Weak transcription	Small Intestine	intestine
5	chr13:95671400-95722200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:95672800-95729000	Weak transcription	Colonic Mucosa	Colon
7	chr13:95676000-95740000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:95677800-95718200	Weak transcription	HSMM	muscle
9	chr13:95682000-95718200	Weak transcription	Pancreas	Pancrea
10	chr13:95682800-95721800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:95683200-95751800	Weak transcription	Fetal Lung	lung
12	chr13:95683800-95725800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr13:95684400-95728200	Weak transcription	Adipose Nuclei	Adipose
14	chr13:95684600-95725400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:95685000-95721400	Weak transcription	Fetal Intestine Small	intestine
16	chr13:95685200-95734600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr13:95686800-95722600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr13:95686800-95744600	Weak transcription	Esophagus	oesophagus
19	chr13:95687000-95722600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr13:95688600-95711400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr13:95691200-95710000	Weak transcription	Aorta	Aorta
22	chr13:95691200-95722400	Weak transcription	Fetal Stomach	stomach
23	chr13:95691600-95711200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr13:95692000-95711200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:95692000-95722400	Weak transcription	Spleen	Spleen
26	chr13:95692200-95722800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr13:95692600-95721200	Weak transcription	Ovary	ovary
28	chr13:95692600-95725600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr13:95692800-95735800	Weak transcription	NHEK	skin
30	chr13:95693800-95722600	Weak transcription	Fetal Intestine Large	intestine
31	chr13:95694400-95718800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr13:95694600-95718000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr13:95694800-95709800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:95694800-95710000	Weak transcription	NHLF	lung
35	chr13:95694800-95711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr13:95694800-95721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:95694800-95721800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr13:95694800-95725600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr13:95695000-95713400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr13:95695000-95722000	Weak transcription	Lung	lung
41	chr13:95695000-95722200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr13:95695200-95718200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr13:95695200-95719000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr13:95695400-95713000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr13:95695600-95723800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr13:95695800-95721200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr13:95696000-95726200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr13:95696800-95713200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:95697000-95712400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr13:95697000-95714200	Weak transcription	K562	blood

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