Variant report

Variant	rs11042582
Chromosome Location	chr11:10008797-10008798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10160515	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10770080	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10770082	0.84[CHB][hapmap];0.96[YRI][hapmap]
rs10770084	0.84[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs10770085	0.88[AMR][1000 genomes]
rs10840331	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10840332	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]
rs10840335	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10840339	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840342	0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840346	0.83[CHB][hapmap];0.88[YRI][hapmap]
rs10840357	0.84[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs10840358	0.84[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap]
rs10840363	0.84[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap]
rs10840364	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs10840369	0.80[CHB][hapmap]
rs11042575	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs11042581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042583	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11042598	0.85[AMR][1000 genomes]
rs11042617	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11042621	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs11042622	0.82[CHB][hapmap];0.84[YRI][hapmap]
rs11042633	0.84[JPT][hapmap]
rs12288355	0.84[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs12295754	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360854	0.84[CHB][hapmap];0.96[YRI][hapmap]
rs2403228	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2403230	0.83[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap]
rs2403259	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2403264	0.83[CHB][hapmap]
rs2403268	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4309158	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4466825	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs4509749	0.80[CHB][hapmap]
rs4909918	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4910085	0.85[CEU][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs4910088	0.83[AMR][1000 genomes]
rs4910089	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6483846	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6483860	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6483883	0.91[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66922162	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7119000	0.83[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs7121704	0.83[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap]
rs7126376	0.84[CHB][hapmap]
rs7128698	0.95[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7129239	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7932988	0.84[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap]
rs7933482	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7936351	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7942420	0.81[AMR][1000 genomes]
rs7947588	0.88[AMR][1000 genomes]
rs7950140	0.80[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11042582	RP11-351I24.1	cis	Whole Blood	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
2	chr11:9981000-10020000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:9981200-10009200	Weak transcription	Brain Germinal Matrix	brain
4	chr11:9981400-10008800	Weak transcription	Primary T cells from cord blood	blood
5	chr11:9981400-10010200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr11:9981400-10014800	Weak transcription	Dnd41	blood
7	chr11:9981400-10017000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:9981400-10051600	Weak transcription	Aorta	Aorta
9	chr11:9983600-10023200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:9984600-10010200	Weak transcription	Fetal Kidney	kidney
11	chr11:9985800-10021600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:9985800-10023600	Weak transcription	Primary B cells from cord blood	blood
13	chr11:9985800-10049000	Weak transcription	Left Ventricle	heart
14	chr11:9990000-10012600	Weak transcription	Liver	Liver
15	chr11:9990000-10018200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:9990400-10028200	Weak transcription	Fetal Brain Female	brain
17	chr11:9991200-10060000	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:9994800-10041800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:9995000-10008800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr11:9996000-10024600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr11:9999600-10010200	Weak transcription	Adipose Nuclei	Adipose
22	chr11:9999600-10019800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr11:9999800-10009800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:9999800-10024000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:9999800-10024200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:10001400-10066200	Weak transcription	Pancreas	Pancrea
27	chr11:10002800-10016000	Weak transcription	Colonic Mucosa	Colon
28	chr11:10003800-10014800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:10004000-10020000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:10004200-10048600	Weak transcription	Brain Angular Gyrus	brain
31	chr11:10004400-10008800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:10004400-10008800	Weak transcription	HSMMtube	muscle
33	chr11:10004400-10020200	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:10004400-10021600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:10004400-10024200	Weak transcription	NHLF	lung
36	chr11:10004600-10010600	Weak transcription	NHDF-Ad	bronchial
37	chr11:10004600-10021800	Weak transcription	Esophagus	oesophagus
38	chr11:10004600-10024000	Weak transcription	Brain Anterior Caudate	brain
39	chr11:10004600-10027600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr11:10004800-10011000	Strong transcription	Fetal Lung	lung
41	chr11:10004800-10021800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:10004800-10023000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr11:10004800-10023800	Weak transcription	HUVEC	blood vessel
44	chr11:10004800-10023800	Weak transcription	Osteobl	bone
45	chr11:10004800-10024800	Weak transcription	HSMM	muscle
46	chr11:10005000-10024000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr11:10005200-10010200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:10005200-10010600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:10005200-10010600	Weak transcription	HepG2	liver
50	chr11:10005200-10012000	Weak transcription	Brain Substantia Nigra	brain

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