Variant report

Variant	rs9985964
Chromosome Location	chr4:110483690-110483691
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10000545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10002595	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10005355	0.83[ASN][1000 genomes]
rs10155127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10213562	0.81[CEU][hapmap]
rs10516558	0.83[ASN][1000 genomes]
rs11098033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11098035	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11929713	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11930655	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11935629	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11941206	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11942291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11942858	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11943384	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11943430	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12642304	0.83[ASN][1000 genomes]
rs12643055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12643844	0.83[ASN][1000 genomes]
rs12644055	0.82[CHB][hapmap]
rs12648138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12648965	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12650654	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13103034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13123618	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13128124	0.83[ASN][1000 genomes]
rs13134239	0.83[ASN][1000 genomes]
rs13141701	0.83[ASN][1000 genomes]
rs13142698	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs13143825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13145066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1509314	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1509315	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17040436	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17040439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17040461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17040488	0.83[ASN][1000 genomes]
rs17040510	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs17040528	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17040543	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17585970	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17619262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28681408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34153531	0.83[ASN][1000 genomes]
rs34224638	0.83[ASN][1000 genomes]
rs34274964	0.83[ASN][1000 genomes]
rs35110951	0.83[ASN][1000 genomes]
rs35594044	0.83[ASN][1000 genomes]
rs35762958	0.83[ASN][1000 genomes]
rs35940980	0.83[ASN][1000 genomes]
rs36115572	0.83[ASN][1000 genomes]
rs3775962	0.83[ASN][1000 genomes]
rs61242473	0.81[ASN][1000 genomes]
rs66667140	0.83[ASN][1000 genomes]
rs67473696	0.81[ASN][1000 genomes]
rs68041341	0.83[ASN][1000 genomes]
rs6812469	0.83[ASN][1000 genomes]
rs6815455	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6818911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6821382	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6821729	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6823032	0.83[ASN][1000 genomes]
rs6827006	0.83[ASN][1000 genomes]
rs6833753	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6835683	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6841198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6845371	0.83[ASN][1000 genomes]
rs6852037	0.83[ASN][1000 genomes]
rs6856291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6856446	0.83[ASN][1000 genomes]
rs73838809	0.83[ASN][1000 genomes]
rs7436583	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7436745	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7440570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7675602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7679836	0.83[ASN][1000 genomes]
rs7687245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9985632	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9994676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9994985	0.83[ASN][1000 genomes]
rs9999570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110482200-110484800	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr4:110482200-110485200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr4:110482400-110483800	Flanking Active TSS	Dnd41	blood
4	chr4:110482400-110484200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:110482400-110485200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:110482600-110483800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:110482600-110483800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:110482600-110484200	Flanking Active TSS	GM12878-XiMat	blood
9	chr4:110482600-110484600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr4:110482800-110483800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:110482800-110484000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:110482800-110484000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr4:110482800-110484000	Enhancers	Primary hematopoietic stem cells	blood
14	chr4:110482800-110484200	Enhancers	Primary B cells from peripheral blood	blood
15	chr4:110482800-110484200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:110482800-110484200	Enhancers	Fetal Brain Male	brain
17	chr4:110482800-110484200	Enhancers	NHEK	skin
18	chr4:110482800-110484400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:110482800-110484600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr4:110482800-110484800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr4:110482800-110494400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:110482800-110495400	Weak transcription	Stomach Mucosa	stomach
23	chr4:110483000-110484000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:110483000-110484000	Enhancers	Primary B cells from cord blood	blood
25	chr4:110483000-110484000	Weak transcription	Fetal Brain Female	brain
26	chr4:110483000-110484200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:110483000-110484200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:110483000-110484400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:110483000-110484600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:110483000-110484800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr4:110483000-110484800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:110483000-110484800	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr4:110483000-110498200	Weak transcription	HMEC	breast
34	chr4:110483200-110484400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr4:110483200-110484400	Enhancers	Thymus	Thymus
36	chr4:110483200-110494400	Weak transcription	NHLF	lung
37	chr4:110483400-110483800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr4:110483400-110484200	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr4:110483400-110484200	Weak transcription	HUVEC	blood vessel
40	chr4:110483400-110484400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:110483400-110484400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:110483400-110484400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr4:110483400-110484400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr4:110483400-110485600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr4:110483400-110486000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr4:110483400-110486200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:110483400-110487000	Weak transcription	NHDF-Ad	bronchial
48	chr4:110483400-110490000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:110483400-110494000	Weak transcription	HSMM	muscle
50	chr4:110483600-110484000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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