Variant report

Variant	rs1189438
Chromosome Location	chr13:95734990-95734991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95733369..95735301-chr13:95738025..95740339,3	K562	blood:
2	chr13:95733801..95735759-chr13:95738839..95740442,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1189430	0.85[EUR][1000 genomes]
rs1189431	0.85[EUR][1000 genomes]
rs1189433	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1189434	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1189435	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1189436	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1189437	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1189439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1189440	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1189451	0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1189452	0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1189453	0.80[ASN][1000 genomes]
rs1189456	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1189461	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1189462	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1189463	0.87[EUR][1000 genomes]
rs1189464	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1189466	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1189467	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1612388	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1617888	0.81[AFR][1000 genomes]
rs1629441	0.90[EUR][1000 genomes]
rs1630901	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1678339	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678341	0.90[CHD][hapmap];0.80[JPT][hapmap]
rs1678347	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1678351	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1678353	1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1678362	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678365	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1678387	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1678395	0.86[CHD][hapmap]
rs1678409	1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs1729745	1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs1729747	0.85[JPT][hapmap]
rs1729752	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1729753	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1729755	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1729773	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1751031	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1751033	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1751036	1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs1751037	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1751042	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1751043	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1751046	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1751052	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1751055	1.00[CEU][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1751056	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1751057	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2619308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2619311	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2619312	0.86[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2766475	1.00[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2766479	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2950957	1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs4148540	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs4773840	0.89[CHD][hapmap];0.80[JPT][hapmap]
rs7330330	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs7331488	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs7338853	0.84[ASN][1000 genomes]
rs7986666	0.94[ASN][1000 genomes]
rs7987858	0.85[ASN][1000 genomes]
rs7988310	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs931111	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs943289	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524790	0.84[ASN][1000 genomes]
rs9561765	0.82[CEU][hapmap];0.82[TSI][hapmap]

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
rs1189438	SNORA70D	trans	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95669600-95744000	Weak transcription	Small Intestine	intestine
2	chr13:95676000-95740000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:95683200-95751800	Weak transcription	Fetal Lung	lung
4	chr13:95686800-95744600	Weak transcription	Esophagus	oesophagus
5	chr13:95692800-95735800	Weak transcription	NHEK	skin
6	chr13:95702400-95735200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr13:95710400-95741200	Weak transcription	Right Ventricle	heart
8	chr13:95718000-95741800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr13:95719600-95739800	Weak transcription	Pancreas	Pancrea
10	chr13:95720000-95735400	Weak transcription	HUVEC	blood vessel
11	chr13:95720000-95736200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr13:95720600-95735000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:95720600-95736600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr13:95723000-95742200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:95723800-95760000	Weak transcription	Colon Smooth Muscle	Colon
16	chr13:95724000-95740000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:95724000-95751800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr13:95724000-95760600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr13:95724200-95740000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr13:95724200-95749600	Weak transcription	Fetal Intestine Large	intestine
21	chr13:95726400-95739800	Weak transcription	NH-A	brain
22	chr13:95727000-95739800	Weak transcription	NHLF	lung
23	chr13:95727000-95752600	Weak transcription	HSMM	muscle
24	chr13:95727000-95791600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:95727000-95812000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr13:95727200-95735000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:95727200-95740000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr13:95727400-95736000	Weak transcription	NHDF-Ad	bronchial
29	chr13:95727600-95761000	Weak transcription	K562	blood
30	chr13:95727800-95744200	Weak transcription	Spleen	Spleen
31	chr13:95727800-95767800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr13:95728400-95778800	Weak transcription	Ovary	ovary
33	chr13:95728600-95744200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr13:95728600-95776000	Weak transcription	Gastric	stomach
35	chr13:95730800-95740000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr13:95731200-95791600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr13:95731600-95756000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr13:95731600-95756600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:95732000-95739800	Weak transcription	GM12878-XiMat	blood
40	chr13:95732800-95751800	Weak transcription	Primary T cells from cord blood	blood
41	chr13:95733000-95736000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr13:95733600-95736600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr13:95733600-95750000	Weak transcription	Lung	lung
44	chr13:95733800-95737400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr13:95733800-95742000	Weak transcription	Aorta	Aorta
46	chr13:95733800-95750000	Weak transcription	Fetal Intestine Small	intestine
47	chr13:95733800-95751600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr13:95734000-95736200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr13:95734000-95737800	Weak transcription	A549	lung
50	chr13:95734600-95735200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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