Variant report

Variant	rs334353
Chromosome Location	chr9:101908365-101908366
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101866534..101869508-chr9:101907295..101910821,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1013186	0.94[CEU][hapmap]
rs10283455	0.94[CEU][hapmap]
rs10448292	0.86[EUR][1000 genomes]
rs10733708	0.87[ASN][1000 genomes]
rs10733709	0.94[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10739778	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10739779	0.94[CEU][hapmap]
rs10760668	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10760669	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10760670	0.87[ASW][hapmap];0.89[CEU][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10760671	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10760672	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10760673	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10760674	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10819634	0.80[ASN][1000 genomes]
rs10819635	0.87[ASW][hapmap];0.83[MEX][hapmap]
rs10819636	0.95[ASN][1000 genomes]
rs10819638	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10819639	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10819640	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs10988706	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10988709	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs10988713	0.81[ASN][1000 genomes]
rs10988715	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs10988716	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10988717	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs10988723	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11568752	1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs11568753	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs11568770	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs11568778	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs12345675	0.93[EUR][1000 genomes]
rs12346650	0.87[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs12685571	1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs1571589	0.89[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1571590	0.94[CEU][hapmap]
rs1590	0.95[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1626340	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1699413	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1888225	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs1973518	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2026811	0.87[ASW][hapmap];0.89[CEU][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs334348	0.95[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334349	0.80[ASW][hapmap];0.95[CEU][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334351	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334354	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs334355	0.87[ASW][hapmap];0.89[CEU][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs334356	0.94[CEU][hapmap]
rs334357	0.94[CEU][hapmap]
rs334358	0.94[CEU][hapmap]
rs334362	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs334363	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs334364	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs334365	0.82[ASN][1000 genomes]
rs334366	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs334367	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs334368	0.89[EUR][1000 genomes]
rs334369	0.91[EUR][1000 genomes]
rs334370	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs334371	0.81[ASN][1000 genomes]
rs367568	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3739798	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs383496	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs401186	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs420549	0.94[CEU][hapmap]
rs44466	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs478061	0.90[EUR][1000 genomes]
rs597457	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6478972	0.87[ASW][hapmap];0.89[CEU][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6478973	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7031302	0.82[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7031309	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7041311	0.91[CHB][hapmap]
rs7042852	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7043624	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7874221	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs868	0.94[CEU][hapmap]

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	nsv893619	chr9:101835165-101936231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS 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	20 gene(s)	inside rSNPs	diseases
3	esv1792736	chr9:101891126-101909372	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Age-related macular degeneration	23455636	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs334353	LOC286359	cis	parietal	SCAN
rs334353	TGFBR1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101870000-101908600	Weak transcription	Brain Germinal Matrix	brain
2	chr9:101890000-101914200	Weak transcription	Pancreas	Pancrea
3	chr9:101890400-101908400	Weak transcription	Hela-S3	cervix
4	chr9:101890600-101908800	Weak transcription	Right Ventricle	heart
5	chr9:101892600-101914200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:101892800-101921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:101895000-101914200	Weak transcription	Esophagus	oesophagus
8	chr9:101897600-101913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:101897600-101915400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:101898000-101912200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:101898000-101919400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:101899000-101913000	Strong transcription	HSMM	muscle
13	chr9:101899400-101913000	Weak transcription	Thymus	Thymus
14	chr9:101900200-101914800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr9:101900200-101915200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:101900800-101916800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr9:101901800-101912000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:101902200-101911200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:101902800-101914200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:101902800-101915400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr9:101903000-101911000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:101903000-101911800	Strong transcription	Fetal Muscle Leg	muscle
23	chr9:101903000-101915200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr9:101903000-101921800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:101903200-101910400	Strong transcription	K562	blood
26	chr9:101903200-101911000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:101903200-101912000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:101903200-101912000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr9:101903200-101912600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:101903200-101913200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr9:101903200-101915000	Strong transcription	Osteobl	bone
32	chr9:101903400-101911400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:101903400-101911400	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:101903400-101914200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr9:101903400-101915400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:101903600-101908800	Strong transcription	Primary T cells from cord blood	blood
37	chr9:101903600-101909400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:101903600-101910800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr9:101903600-101911000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr9:101903600-101911400	Strong transcription	Dnd41	blood
41	chr9:101903600-101912200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:101903600-101915000	Strong transcription	HSMMtube	muscle
43	chr9:101903600-101915200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:101903800-101909800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:101903800-101911400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:101903800-101911600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:101903800-101912000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr9:101903800-101913000	Strong transcription	Adipose Nuclei	Adipose
49	chr9:101904000-101910800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:101904000-101911800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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