Variant report

Variant	rs11196871
Chromosome Location	chr10:116443036-116443037
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11196844	0.83[YRI][hapmap]
rs11196845	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs11196853	0.92[YRI][hapmap]
rs11196858	1.00[AFR][1000 genomes]
rs11196861	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11196866	1.00[ASN][1000 genomes]
rs11196868	1.00[ASN][1000 genomes]
rs11196869	1.00[CEU][hapmap]
rs11196870	1.00[ASN][1000 genomes]
rs11196878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196880	1.00[ASN][1000 genomes]
rs12782152	1.00[ASN][1000 genomes]
rs217190	1.00[CEU][hapmap]
rs217191	1.00[CEU][hapmap]
rs217193	1.00[ASN][1000 genomes]
rs217195	1.00[ASN][1000 genomes]
rs217196	1.00[ASN][1000 genomes]
rs217197	1.00[ASN][1000 genomes]
rs7091958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11196871	RPL13AP6	cis	parietal	SCAN
rs11196871	GFRA1	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116431600-116444000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:116435000-116444000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr10:116438600-116444800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr10:116439000-116444000	Weak transcription	NHDF-Ad	bronchial
5	chr10:116439000-116444600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr10:116439200-116443400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:116439800-116444000	Enhancers	Fetal Lung	lung
8	chr10:116440600-116443200	Enhancers	HMEC	breast
9	chr10:116441200-116443200	Enhancers	HSMM	muscle
10	chr10:116441200-116444000	Enhancers	Stomach Mucosa	stomach
11	chr10:116441200-116445200	Flanking Active TSS	HUVEC	blood vessel
12	chr10:116441400-116443200	Enhancers	Fetal Intestine Large	intestine
13	chr10:116441400-116443200	Enhancers	Fetal Stomach	stomach
14	chr10:116441400-116443800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:116441400-116444000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr10:116441400-116444000	Flanking Active TSS	Fetal Heart	heart
17	chr10:116441400-116444200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr10:116441400-116444400	Active TSS	Psoas Muscle	Psoas
19	chr10:116441400-116445600	Enhancers	Fetal Brain Male	brain
20	chr10:116441400-116446200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:116441600-116443400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr10:116441600-116443600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:116441600-116444200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr10:116441600-116444600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:116441800-116443200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:116441800-116443200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:116441800-116443200	Weak transcription	Fetal Muscle Leg	muscle
28	chr10:116441800-116443200	Weak transcription	Pancreas	Pancrea
29	chr10:116441800-116443200	Weak transcription	Spleen	Spleen
30	chr10:116441800-116443200	Enhancers	HSMMtube	muscle
31	chr10:116441800-116443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr10:116441800-116443400	Weak transcription	Gastric	stomach
33	chr10:116441800-116443400	Active TSS	Right Atrium	heart
34	chr10:116441800-116443400	Weak transcription	Hela-S3	cervix
35	chr10:116441800-116443600	Active TSS	Right Ventricle	heart
36	chr10:116441800-116444000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:116441800-116444000	Active TSS	Adipose Nuclei	Adipose
38	chr10:116441800-116444000	Active TSS	Left Ventricle	heart
39	chr10:116441800-116444000	Weak transcription	Ovary	ovary
40	chr10:116441800-116445200	Weak transcription	Brain Angular Gyrus	brain
41	chr10:116441800-116445600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr10:116441800-116450800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:116442000-116443400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:116442000-116443400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr10:116442000-116444400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:116442000-116444400	Flanking Active TSS	Fetal Brain Female	brain
47	chr10:116442200-116443200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr10:116442200-116443600	Bivalent Enhancer	Brain Hippocampus Middle	brain
49	chr10:116442200-116444000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr10:116442400-116443200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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