Variant report

Variant	rs2233177
Chromosome Location	chr9:5892375-5892376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10975331	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10975334	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12337445	0.80[YRI][hapmap]
rs12339889	0.85[CHD][hapmap]
rs12342282	1.00[CHD][hapmap]
rs12350407	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411948	1.00[MEX][hapmap]
rs1993912	0.85[CHD][hapmap]
rs2233173	0.86[ASW][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap]
rs2233178	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59103465	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73391389	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73391390	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73395357	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1033546	chr9:5875201-5900427	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5840400-5921600	Weak transcription	Right Ventricle	heart
2	chr9:5852200-5897000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr9:5853800-5895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:5856800-5895600	Weak transcription	Brain Substantia Nigra	brain
5	chr9:5859000-5895600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:5859000-5906600	Weak transcription	Ovary	ovary
7	chr9:5859200-5919800	Weak transcription	Fetal Brain Female	brain
8	chr9:5863400-5895600	Weak transcription	Fetal Intestine Small	intestine
9	chr9:5863600-5896600	Weak transcription	Pancreas	Pancrea
10	chr9:5864800-5895600	Weak transcription	Gastric	stomach
11	chr9:5870800-5895600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:5871000-5895600	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:5871000-5920000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:5871200-5898400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:5877000-5895600	Weak transcription	Left Ventricle	heart
16	chr9:5877000-5896000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:5877200-5894200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:5877200-5895400	Weak transcription	Fetal Stomach	stomach
19	chr9:5877200-5895600	Weak transcription	Aorta	Aorta
20	chr9:5882200-5896200	Weak transcription	Spleen	Spleen
21	chr9:5882400-5895400	Weak transcription	Primary T cells from cord blood	blood
22	chr9:5883000-5906400	Weak transcription	Fetal Brain Male	brain
23	chr9:5884600-5910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:5885800-5898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:5886400-5893200	Weak transcription	Placenta	Placenta
26	chr9:5886600-5895600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr9:5886600-5895600	Weak transcription	Right Atrium	heart
28	chr9:5886600-5895800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:5886600-5896600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr9:5886600-5897200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:5886800-5896000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:5886800-5905000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr9:5886800-5920400	Weak transcription	GM12878-XiMat	blood
34	chr9:5886800-5920600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr9:5886800-5922000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr9:5887000-5895600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr9:5887000-5895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:5887000-5921600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr9:5887400-5896800	Weak transcription	Brain Germinal Matrix	brain
40	chr9:5887600-5892400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:5889000-5898400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr9:5890600-5892400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:5891000-5893400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:5891000-5895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:5891200-5893400	Enhancers	HepG2	liver
46	chr9:5891400-5893400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:5891600-5893200	Enhancers	Primary hematopoietic stem cells	blood
48	chr9:5891800-5892400	Enhancers	K562	blood
49	chr9:5891800-5893000	Enhancers	Thymus	Thymus
50	chr9:5891800-5893400	Enhancers	Fetal Thymus	thymus

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