Variant report

Variant	rs3824473
Chromosome Location	chr9:104334777-104334778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104332352..104334996-chr9:104342895..104344528,3	MCF-7	breast:
2	chr9:104329440..104331713-chr9:104334657..104336622,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10115763	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10989553	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12342026	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343288	0.85[ASN][1000 genomes]
rs12347518	0.96[ASN][1000 genomes]
rs1323433	0.82[JPT][hapmap]
rs13290720	0.85[CHD][hapmap]
rs16920473	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1885977	0.87[ASN][1000 genomes]
rs1929496	0.85[CHD][hapmap]
rs34153995	0.87[ASN][1000 genomes]
rs34727333	0.85[ASN][1000 genomes]
rs36004060	0.85[ASN][1000 genomes]
rs3739722	0.99[ASN][1000 genomes]
rs3739723	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs3739724	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs45488691	0.89[ASN][1000 genomes]
rs7023041	0.80[AMR][1000 genomes]
rs7030238	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7034754	0.86[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7858998	0.82[JPT][hapmap]
rs9299345	0.96[ASN][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	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	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
3	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
4	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:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104296800-104337400	Weak transcription	Stomach Mucosa	stomach
2	chr9:104313200-104335400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:104323600-104334800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:104324800-104334800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:104324800-104334800	Weak transcription	Right Ventricle	heart
6	chr9:104325200-104344400	Weak transcription	NHLF	lung
7	chr9:104325200-104350000	Weak transcription	HSMMtube	muscle
8	chr9:104326800-104337000	Weak transcription	Esophagus	oesophagus
9	chr9:104327000-104336200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:104327000-104336400	Weak transcription	Brain Germinal Matrix	brain
11	chr9:104327000-104338400	Weak transcription	Gastric	stomach
12	chr9:104327000-104344600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:104327400-104339600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:104327400-104348400	Weak transcription	Aorta	Aorta
15	chr9:104327600-104337000	Weak transcription	Pancreas	Pancrea
16	chr9:104327600-104337600	Weak transcription	HepG2	liver
17	chr9:104327600-104344400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:104327800-104338400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:104327800-104344400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:104328000-104334800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:104328000-104342200	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:104328400-104340600	Weak transcription	GM12878-XiMat	blood
23	chr9:104329000-104338800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr9:104329200-104335200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr9:104329400-104337400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr9:104329400-104337800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:104329400-104338200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr9:104330200-104338600	Weak transcription	Colonic Mucosa	Colon
29	chr9:104330400-104337400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr9:104330800-104336400	Weak transcription	Fetal Brain Female	brain
31	chr9:104331000-104335400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr9:104331400-104335600	Enhancers	K562	blood
33	chr9:104331600-104336400	Weak transcription	Fetal Brain Male	brain
34	chr9:104331800-104337000	Weak transcription	Left Ventricle	heart
35	chr9:104331800-104337200	Weak transcription	Brain Angular Gyrus	brain
36	chr9:104331800-104337400	Enhancers	Primary T cells fromperipheralblood	blood
37	chr9:104331800-104344600	Weak transcription	HSMM	muscle
38	chr9:104332400-104336600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:104332400-104338800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:104332400-104344600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:104332800-104335200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr9:104332800-104335600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr9:104332800-104335800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr9:104332800-104336000	Enhancers	H9 Cell Line	embryonic stem cell
45	chr9:104332800-104340600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr9:104333000-104334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:104333000-104335400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr9:104333000-104335400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:104333000-104335400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:104333000-104335600	Enhancers	Primary T helper cells PMA-I stimulated	--

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