Variant report

Variant	rs10840332
Chromosome Location	chr11:9980501-9980502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10160515	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10734652	0.80[ASW][hapmap]
rs10770080	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10770082	0.96[YRI][hapmap]
rs10770084	0.81[JPT][hapmap];0.96[YRI][hapmap]
rs10770085	0.81[AMR][1000 genomes]
rs10840331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840339	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10840342	0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs10840346	0.86[ASW][hapmap];0.88[YRI][hapmap]
rs10840357	0.85[JPT][hapmap];0.92[YRI][hapmap]
rs10840358	0.81[JPT][hapmap];0.92[YRI][hapmap]
rs10840363	0.81[JPT][hapmap];0.92[YRI][hapmap]
rs10840364	0.80[JPT][hapmap]
rs11042564	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042575	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11042581	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042582	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042617	0.80[ASW][hapmap];0.81[JPT][hapmap]
rs11042621	0.81[JPT][hapmap]
rs11042622	0.82[YRI][hapmap]
rs11042633	0.82[JPT][hapmap]
rs12288355	0.81[JPT][hapmap];0.96[YRI][hapmap]
rs12295754	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12360854	0.96[YRI][hapmap]
rs2403228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2403230	0.86[ASW][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap]
rs2403259	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs4309158	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4910085	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4910088	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4910089	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6483846	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6483860	0.95[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6483883	0.86[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs6483966	0.80[ASW][hapmap]
rs66922162	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7102016	0.86[ASW][hapmap];0.83[CHB][hapmap];0.95[MEX][hapmap]
rs7110312	0.80[ASW][hapmap]
rs7119000	0.86[ASW][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap]
rs7121704	0.86[ASW][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap]
rs7128698	0.86[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs7129239	0.86[AMR][1000 genomes]
rs7932988	0.92[YRI][hapmap]
rs7933482	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7936351	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7939451	0.81[EUR][1000 genomes]
rs7947588	0.81[AMR][1000 genomes]
rs7950140	0.83[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv1819684	chr11:9973062-10012511	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv982983	chr11:9980342-9981342	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840332	RP11-351I24.1	cis	Whole Blood	GTEx
rs10840332	SYT9	cis	cerebellum	SCAN
rs10840332	OR52B2	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9943400-9980600	Weak transcription	Primary T cells from cord blood	blood
2	chr11:9952800-9980600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:9952800-9980600	Weak transcription	Spleen	Spleen
4	chr11:9952800-9995200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:9965200-9981000	Weak transcription	HUVEC	blood vessel
6	chr11:9968000-9984000	Weak transcription	Primary B cells from cord blood	blood
7	chr11:9968000-9984200	Weak transcription	Fetal Kidney	kidney
8	chr11:9972800-9980600	Weak transcription	Gastric	stomach
9	chr11:9973000-9986000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
11	chr11:9974200-9980800	Weak transcription	Brain Germinal Matrix	brain
12	chr11:9974200-9994400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:9974200-9994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:9974200-9994800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:9974200-9999000	Weak transcription	Fetal Heart	heart
16	chr11:9974200-9999000	Weak transcription	HSMMtube	muscle
17	chr11:9974400-9980600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:9974400-9982800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:9975400-9985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:9975600-9981000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr11:9977000-9994400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:9977600-9982000	Weak transcription	Stomach Mucosa	stomach
23	chr11:9977800-9981600	Strong transcription	Fetal Lung	lung
24	chr11:9978200-9981600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:9978600-9981800	Strong transcription	Left Ventricle	heart
26	chr11:9978600-9986000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:9978800-9980600	Weak transcription	HMEC	breast
28	chr11:9978800-9985000	Weak transcription	Small Intestine	intestine
29	chr11:9979200-9980600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:9979400-9981600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:9979400-9982000	Weak transcription	Colonic Mucosa	Colon
32	chr11:9979400-9986000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr11:9979400-9995000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr11:9979600-9981600	Strong transcription	Fetal Muscle Leg	muscle
35	chr11:9979600-9981800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:9979600-9982000	Strong transcription	Fetal Stomach	stomach
37	chr11:9979600-9985600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:9979600-9985800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:9979600-9994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:9979800-9981200	Weak transcription	Lung	lung
41	chr11:9979800-9987400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:9979800-9999200	Weak transcription	NH-A	brain
43	chr11:9980000-9981600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:9980000-9982200	Weak transcription	Thymus	Thymus
45	chr11:9980200-9980800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:9980200-9980800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:9980200-9981000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr11:9980200-9981000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:9980200-9981200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:9980200-9981200	Strong transcription	NHDF-Ad	bronchial

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