Variant report

Variant	rs10989553
Chromosome Location	chr9:104315931-104315932
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10115763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12342026	0.96[ASN][1000 genomes]
rs12343288	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12347518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13284984	0.81[JPT][hapmap]
rs13290720	0.85[CHD][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap]
rs16920473	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.88[ASN][1000 genomes]
rs1885977	0.86[ASN][1000 genomes]
rs1929496	0.85[CHD][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap]
rs28736702	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34153995	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs34727333	0.88[ASN][1000 genomes]
rs36004060	0.88[ASN][1000 genomes]
rs3739722	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3739723	0.82[CHD][hapmap];0.94[JPT][hapmap]
rs3739724	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs3824473	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs45488691	0.85[ASN][1000 genomes]
rs7030238	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7034754	0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9299345	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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 target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv831672	chr9:104300755-104480849	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104296800-104334200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:104296800-104337400	Weak transcription	Stomach Mucosa	stomach
3	chr9:104297000-104317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:104297600-104321200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:104297600-104330400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:104297600-104330400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:104297800-104317400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:104297800-104318400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr9:104297800-104320400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:104297800-104320400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:104297800-104325400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr9:104297800-104332600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:104297800-104333000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:104298000-104332800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr9:104298200-104328200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr9:104298200-104333200	Strong transcription	Adipose Nuclei	Adipose
17	chr9:104298400-104320000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:104298400-104333200	Strong transcription	Liver	Liver
19	chr9:104298400-104333400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr9:104298600-104325000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:104298800-104317600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr9:104299000-104333000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:104299200-104324200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:104299200-104330400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:104299600-104321000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr9:104300800-104323400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:104300800-104327000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:104301000-104320200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:104301200-104328800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:104301400-104323800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:104301600-104333400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:104301800-104320400	Strong transcription	Fetal Brain Female	brain
33	chr9:104301800-104331800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:104302000-104317200	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr9:104302200-104316400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr9:104302200-104320800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:104302200-104333000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr9:104302600-104317200	Strong transcription	Brain Anterior Caudate	brain
39	chr9:104302600-104317200	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:104302800-104318000	Strong transcription	Placenta	Placenta
41	chr9:104305200-104318400	Strong transcription	Primary T cells from cord blood	blood
42	chr9:104305400-104316600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr9:104305400-104316600	Strong transcription	Fetal Muscle Leg	muscle
44	chr9:104305400-104320600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:104305600-104318200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:104305600-104320600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr9:104305600-104321600	Strong transcription	Dnd41	blood
48	chr9:104305600-104325200	Strong transcription	Brain Hippocampus Middle	brain
49	chr9:104305600-104328600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:104305800-104316600	Strong transcription	Fetal Thymus	thymus

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