Variant report

Variant	rs11006884
Chromosome Location	chr10:28409974-28409975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10826397	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10826398	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11006818	0.97[AMR][1000 genomes]
rs11006820	0.82[AMR][1000 genomes]
rs11006821	0.82[AMR][1000 genomes]
rs11006822	0.92[AMR][1000 genomes]
rs11006823	0.92[AMR][1000 genomes]
rs11006825	0.97[AMR][1000 genomes]
rs11006826	0.82[AMR][1000 genomes]
rs11006827	0.92[AMR][1000 genomes]
rs11006830	0.82[AMR][1000 genomes]
rs11006832	0.98[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11006833	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11006834	0.98[AMR][1000 genomes]
rs11006836	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11006839	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11006840	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11006841	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11006843	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11006855	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11006863	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11006867	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11006869	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11006870	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11006873	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11006877	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11006880	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006881	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11006883	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12219860	0.93[AMR][1000 genomes]
rs12220659	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1317790	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17757844	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2887213	0.97[AMR][1000 genomes]
rs3885634	0.82[AMR][1000 genomes]
rs3885635	0.88[AMR][1000 genomes]
rs56163384	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56349465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57764949	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59082756	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59246203	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6481499	0.90[AMR][1000 genomes]
rs7071369	0.97[AMR][1000 genomes]
rs72801890	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7895285	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs927676	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv894988	chr10:28337570-28410989	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1848511	chr10:28373644-28464753	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1851923	chr10:28384098-28410989	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv894989	chr10:28384098-28449974	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv949151	chr10:28386125-28455221	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1845096	chr10:28405411-28423204	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28347000-28412200	Weak transcription	Left Ventricle	heart
2	chr10:28347000-28414600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:28364800-28416600	Weak transcription	Pancreas	Pancrea
4	chr10:28367800-28420200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:28376000-28438400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr10:28376600-28416600	Weak transcription	Fetal Intestine Large	intestine
7	chr10:28378000-28418400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:28378600-28412800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:28378600-28425600	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:28379200-28416600	Weak transcription	Fetal Intestine Small	intestine
11	chr10:28389600-28416400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr10:28392200-28417000	Weak transcription	Esophagus	oesophagus
13	chr10:28392400-28416800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:28396200-28414400	Weak transcription	Adipose Nuclei	Adipose
15	chr10:28396400-28422400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr10:28396800-28416600	Weak transcription	Aorta	Aorta
17	chr10:28398000-28417200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr10:28401800-28414800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr10:28403400-28414800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr10:28403600-28443200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr10:28404800-28416800	Weak transcription	Fetal Stomach	stomach
22	chr10:28406600-28413400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr10:28406600-28421600	Weak transcription	Primary B cells from cord blood	blood
24	chr10:28407000-28413400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:28407400-28410200	Enhancers	Hela-S3	cervix
26	chr10:28407400-28411000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr10:28407400-28413400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr10:28407400-28414200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr10:28407400-28414400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr10:28407600-28410000	Weak transcription	Right Ventricle	heart
31	chr10:28407600-28413200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:28407600-28414200	Strong transcription	Primary T cells from cord blood	blood
33	chr10:28407600-28418800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr10:28407800-28410000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr10:28407800-28411000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr10:28407800-28413600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr10:28407800-28414200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr10:28408200-28415000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr10:28408600-28410000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr10:28408600-28410200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr10:28408800-28410800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr10:28409200-28410400	Strong transcription	HepG2	liver
43	chr10:28409200-28413800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:28409200-28413800	Weak transcription	HSMMtube	muscle
45	chr10:28409200-28416600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr10:28409400-28410200	Flanking Active TSS	Liver	Liver
47	chr10:28409400-28412800	Weak transcription	HSMM	muscle
48	chr10:28409400-28418800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:28409600-28410000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:28409600-28412600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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