Variant report

Variant	rs11195387
Chromosome Location	chr10:112711917-112711918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10082499	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10787286	0.80[CEU][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10787291	0.90[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10787293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10787299	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885059	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10885060	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10885061	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10885064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885071	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885073	0.80[AFR][1000 genomes]
rs10885075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10885076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11195381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11195390	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11195391	0.80[AFR][1000 genomes]
rs11195398	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12240685	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12242177	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12242928	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12246561	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12249031	0.89[AFR][1000 genomes]
rs12253351	0.80[AFR][1000 genomes]
rs12261765	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12358859	0.82[CHB][hapmap]
rs12776359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12776861	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1571239	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17186196	0.83[AFR][1000 genomes]
rs2146544	0.82[YRI][hapmap]
rs34401279	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34893229	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35394459	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35793075	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35946882	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3750619	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3763692	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61864641	0.83[AFR][1000 genomes]
rs6421360	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6585026	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7070962	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7074629	0.89[AFR][1000 genomes]
rs7075507	0.90[ASN][1000 genomes]
rs7089193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7089615	0.90[ASN][1000 genomes]
rs7089687	0.80[CEU][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7096359	1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes]
rs7922142	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9663346	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1051327	chr10:112650316-112772917	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540774	chr10:112650316-112772917	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1047865	chr10:112660427-112730573	Enhancers Weak transcription Active TSS Strong transcription Flanking 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	26 gene(s)	inside rSNPs	diseases
7	nsv1048809	chr10:112683822-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1042020	chr10:112686323-112795159	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11195387	LOC92482	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112682000-112732400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr10:112684400-112712600	Weak transcription	HepG2	liver
3	chr10:112685200-112719200	Weak transcription	A549	lung
4	chr10:112689600-112714400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:112692000-112722000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr10:112692400-112719000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:112692400-112719000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr10:112692400-112724000	Weak transcription	Stomach Mucosa	stomach
9	chr10:112692600-112713600	Weak transcription	Hela-S3	cervix
10	chr10:112692600-112732400	Weak transcription	Fetal Intestine Large	intestine
11	chr10:112693600-112719200	Weak transcription	Small Intestine	intestine
12	chr10:112693600-112722000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr10:112695400-112722400	Weak transcription	Colonic Mucosa	Colon
14	chr10:112697200-112720400	Weak transcription	Ovary	ovary
15	chr10:112697200-112740200	Weak transcription	Thymus	Thymus
16	chr10:112697200-112745400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr10:112698000-112724000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:112700600-112712200	Weak transcription	Fetal Brain Male	brain
19	chr10:112700600-112764000	Weak transcription	Placenta	Placenta
20	chr10:112701200-112726800	Weak transcription	Dnd41	blood
21	chr10:112702200-112722000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr10:112702400-112754800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr10:112703200-112712000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:112703200-112712400	Weak transcription	Fetal Kidney	kidney
25	chr10:112703600-112721400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:112703800-112712200	Weak transcription	Fetal Lung	lung
27	chr10:112703800-112712400	Weak transcription	Fetal Muscle Leg	muscle
28	chr10:112703800-112718200	Weak transcription	Liver	Liver
29	chr10:112703800-112720800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr10:112703800-112724200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:112703800-112725800	Weak transcription	HUVEC	blood vessel
32	chr10:112703800-112729000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr10:112704600-112714600	Weak transcription	Brain Angular Gyrus	brain
34	chr10:112704800-112719000	Weak transcription	Colon Smooth Muscle	Colon
35	chr10:112705200-112712400	Weak transcription	Fetal Thymus	thymus
36	chr10:112705200-112789800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:112705400-112721200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr10:112705600-112713000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:112705600-112713800	Weak transcription	Spleen	Spleen
40	chr10:112705600-112714000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr10:112705800-112712000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr10:112705800-112716800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr10:112705800-112719000	Weak transcription	Adipose Nuclei	Adipose
44	chr10:112705800-112725400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr10:112706600-112712200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr10:112707000-112719000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr10:112707200-112712000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr10:112707200-112712200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr10:112707200-112712400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr10:112707200-112712400	Weak transcription	Esophagus	oesophagus

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