Variant report

Variant	rs11239779
Chromosome Location	chr10:43305660-43305661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10900269	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10900274	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10900275	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239766	0.81[TSI][hapmap]
rs11239767	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11239769	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11239772	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11239786	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11597306	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12049745	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12049769	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12220767	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap]
rs12762093	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12764004	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12771057	0.83[ASN][1000 genomes]
rs17158190	0.84[AFR][1000 genomes]
rs3982199	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949036	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9733285	0.82[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv895076	chr10:43234432-43326627	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1047838	chr10:43234590-43379219	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
14	nsv947891	chr10:43299039-43319274	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv14695	chr10:43301539-43355457	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11239779	HSD17B7P2	cis	parietal	SCAN
rs11239779	MARCH8	cis	cerebellum	SCAN
rs11239779	BMS1	cis	cerebellum	SCAN
rs11239779	HSD17B7P2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43279800-43306200	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr10:43279800-43306400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr10:43279800-43307600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr10:43279800-43307800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr10:43279800-43307800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr10:43279800-43308400	Strong transcription	Fetal Intestine Large	intestine
7	chr10:43279800-43308800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:43279800-43309000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr10:43279800-43324000	Strong transcription	Liver	Liver
10	chr10:43279800-43328200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr10:43280000-43305800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:43280000-43306400	Strong transcription	Placenta	Placenta
13	chr10:43280000-43306400	Strong transcription	A549	lung
14	chr10:43280000-43306800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:43280000-43309600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr10:43280000-43310800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:43280200-43306000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:43280200-43310600	Strong transcription	Primary T cells from cord blood	blood
19	chr10:43281000-43308600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr10:43281800-43306800	Strong transcription	Dnd41	blood
21	chr10:43282400-43308200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr10:43284200-43306400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr10:43284400-43306400	Strong transcription	Primary hematopoietic stem cells	blood
24	chr10:43293000-43307600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr10:43293200-43332400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr10:43294400-43311800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:43294600-43322800	Weak transcription	Stomach Mucosa	stomach
28	chr10:43295000-43308000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:43295000-43309400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:43295600-43311800	Weak transcription	Pancreas	Pancrea
31	chr10:43296600-43307600	Weak transcription	Aorta	Aorta
32	chr10:43296600-43307600	Weak transcription	Spleen	Spleen
33	chr10:43296600-43307800	Weak transcription	Esophagus	oesophagus
34	chr10:43296600-43309400	Weak transcription	Small Intestine	intestine
35	chr10:43296800-43311800	Weak transcription	Colonic Mucosa	Colon
36	chr10:43297800-43307400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr10:43298800-43313000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:43299600-43309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr10:43299600-43309600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr10:43299600-43318600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr10:43299800-43309200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr10:43299800-43312400	Weak transcription	HSMMtube	muscle
43	chr10:43299800-43313000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr10:43300000-43312800	Weak transcription	Fetal Brain Male	brain
45	chr10:43300000-43318000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr10:43300800-43310600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr10:43301000-43305800	Strong transcription	Adipose Nuclei	Adipose
48	chr10:43301200-43308200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr10:43301200-43309200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:43301400-43305800	Strong transcription	Duodenum Mucosa	Duodenum

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