Variant report

Variant	rs7102016
Chromosome Location	chr11:10127309-10127310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10128601	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10500722	0.89[YRI][hapmap]
rs10500724	0.89[CEU][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs10734652	0.93[ASW][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs10770080	0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs10770082	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs10770084	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10770085	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10770087	0.83[ASN][1000 genomes]
rs10770088	0.81[ASN][1000 genomes]
rs10770090	0.81[ASN][1000 genomes]
rs10770096	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10770104	0.81[EUR][1000 genomes]
rs10840331	0.82[CHB][hapmap]
rs10840332	0.86[ASW][hapmap];0.83[CHB][hapmap];0.95[MEX][hapmap]
rs10840335	0.83[CHB][hapmap]
rs10840346	1.00[ASW][hapmap];0.95[CHB][hapmap]
rs10840357	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10840358	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10840363	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10840364	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10840368	0.89[ASN][1000 genomes]
rs10840369	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs11042598	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11042617	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042621	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11042622	0.95[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11042625	0.83[ASN][1000 genomes]
rs11042633	0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11042638	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11042702	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs11042714	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs11602090	0.84[EUR][1000 genomes]
rs11607174	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs12224149	0.81[ASN][1000 genomes]
rs12288355	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12360854	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1442738	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs2083715	0.81[EUR][1000 genomes]
rs2083716	0.83[EUR][1000 genomes]
rs2083717	0.88[EUR][1000 genomes]
rs2403230	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2403259	0.81[CEU][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes]
rs2403264	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2403268	0.85[EUR][1000 genomes]
rs4267063	0.87[EUR][1000 genomes]
rs4309158	0.83[CHB][hapmap]
rs4323860	0.92[CEU][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs4466825	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4482025	0.84[EUR][1000 genomes]
rs4509749	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4597056	0.92[CEU][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs4635071	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4910085	0.80[ASW][hapmap];0.95[MEX][hapmap]
rs4910089	0.95[MEX][hapmap]
rs4910097	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs4910107	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs4910108	0.83[EUR][1000 genomes]
rs4910115	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs56063978	0.80[EUR][1000 genomes]
rs58623593	0.81[ASN][1000 genomes]
rs6483860	0.80[CHB][hapmap]
rs6483883	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6483964	0.82[ASN][1000 genomes]
rs6483965	0.82[ASN][1000 genomes]
rs6483966	0.93[ASW][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs6483970	0.87[ASW][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6484147	0.92[CEU][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs6484148	0.91[CEU][hapmap]
rs6484152	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs7104821	0.82[ASN][1000 genomes]
rs7106328	0.82[ASN][1000 genomes]
rs7106998	0.83[EUR][1000 genomes]
rs7107290	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs7108358	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs7110312	0.93[ASW][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs7110652	0.92[CEU][hapmap]
rs7110664	0.80[ASN][1000 genomes]
rs7115944	1.00[CEU][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs7118500	0.92[CEU][hapmap]
rs7119000	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7121704	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7123728	0.92[CEU][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs7126376	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7128698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7129239	0.84[AMR][1000 genomes]
rs7131203	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs726102	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs7479039	0.92[CEU][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs7924499	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7928170	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7932988	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7938543	0.92[CEU][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs7938891	0.81[ASN][1000 genomes]
rs7939146	0.82[ASN][1000 genomes]
rs7942420	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7947588	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7947666	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs7948166	0.82[ASN][1000 genomes]
rs7950140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv1039636	chr11:10126747-10280570	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7102016	TRIM66	cis	cerebellum	SCAN
rs7102016	ZNF143	cis	cerebellum	SCAN
rs7102016	RP11-351I24.1	cis	Whole Blood	GTEx
rs7102016	OR52B2	cis	parietal	SCAN
rs7102016	SYT9	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10116800-10131000	Weak transcription	Gastric	stomach
2	chr11:10117200-10131000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:10120400-10142800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:10120600-10129200	Weak transcription	Psoas Muscle	Psoas
5	chr11:10120800-10131000	Weak transcription	A549	lung
6	chr11:10121000-10129800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:10121200-10130400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:10121400-10131200	Weak transcription	Liver	Liver
9	chr11:10122200-10129000	Weak transcription	Adipose Nuclei	Adipose
10	chr11:10122200-10129000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:10122200-10130800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:10122200-10131000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:10122200-10144200	Weak transcription	Left Ventricle	heart
14	chr11:10122200-10156400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:10122400-10127800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr11:10122400-10129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:10122400-10130800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:10122400-10130800	Weak transcription	Fetal Lung	lung
19	chr11:10122400-10130800	Weak transcription	HSMM	muscle
20	chr11:10122400-10131200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:10122400-10138600	Weak transcription	Esophagus	oesophagus
22	chr11:10122600-10130400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:10122600-10130800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:10122800-10129000	Weak transcription	NHLF	lung
25	chr11:10122800-10130400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:10122800-10130400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:10122800-10131000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:10122800-10132800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:10122800-10141200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr11:10122800-10142600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:10123000-10130200	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:10123000-10130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:10123200-10156400	Weak transcription	Fetal Intestine Small	intestine
34	chr11:10124800-10128000	Weak transcription	NHDF-Ad	bronchial
35	chr11:10126000-10127400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:10126200-10129000	Weak transcription	Aorta	Aorta
37	chr11:10126200-10129000	Weak transcription	HSMMtube	muscle
38	chr11:10126200-10131000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:10126200-10143000	Weak transcription	Ovary	ovary
40	chr11:10127000-10127400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:10127200-10127400	Enhancers	Right Atrium	heart
42	chr11:10127200-10127600	Enhancers	Fetal Heart	heart

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