Variant report

Variant	rs334356
Chromosome Location	chr9:101909372-101909373
allele	C/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: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1013186	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10283455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10448292	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10733709	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10739779	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760668	0.88[EUR][1000 genomes]
rs10760669	0.89[EUR][1000 genomes]
rs10760670	0.94[CEU][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs10760671	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10760672	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10760673	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10760674	0.89[AFR][1000 genomes]
rs10819635	0.83[CEU][hapmap];0.93[TSI][hapmap]
rs10819637	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819638	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10819639	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10988703	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988706	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10988714	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988716	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10988748	1.00[CHD][hapmap]
rs12345675	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12346650	0.93[TSI][hapmap]
rs13286149	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571589	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs1571590	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1590	0.89[CEU][hapmap]
rs1626340	0.87[EUR][1000 genomes]
rs1699413	0.92[EUR][1000 genomes]
rs2026811	0.94[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs334348	0.89[CEU][hapmap]
rs334349	0.89[CEU][hapmap]
rs334350	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334353	0.94[CEU][hapmap]
rs334354	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs334355	0.94[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs334357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334358	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334362	0.91[EUR][1000 genomes]
rs334368	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs334369	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs367568	0.86[EUR][1000 genomes]
rs385057	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401186	0.86[EUR][1000 genomes]
rs420549	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs44466	0.89[EUR][1000 genomes]
rs478061	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs597457	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6478972	0.94[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs6478973	0.89[EUR][1000 genomes]
rs7031302	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7031309	0.83[EUR][1000 genomes]
rs7042852	0.94[CEU][hapmap]
rs7043624	0.83[CEU][hapmap]
rs7874221	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs789675	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs334356	TGFBR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101890000-101914200	Weak transcription	Pancreas	Pancrea
2	chr9:101892600-101914200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:101892800-101921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:101895000-101914200	Weak transcription	Esophagus	oesophagus
5	chr9:101897600-101913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:101897600-101915400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:101898000-101912200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:101898000-101919400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:101899000-101913000	Strong transcription	HSMM	muscle
10	chr9:101899400-101913000	Weak transcription	Thymus	Thymus
11	chr9:101900200-101914800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr9:101900200-101915200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:101900800-101916800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr9:101901800-101912000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:101902200-101911200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:101902800-101914200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:101902800-101915400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr9:101903000-101911000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:101903000-101911800	Strong transcription	Fetal Muscle Leg	muscle
20	chr9:101903000-101915200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr9:101903000-101921800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr9:101903200-101910400	Strong transcription	K562	blood
23	chr9:101903200-101911000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr9:101903200-101912000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:101903200-101912000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr9:101903200-101912600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr9:101903200-101913200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr9:101903200-101915000	Strong transcription	Osteobl	bone
29	chr9:101903400-101911400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:101903400-101911400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:101903400-101914200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:101903400-101915400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:101903600-101909400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:101903600-101910800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr9:101903600-101911000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr9:101903600-101911400	Strong transcription	Dnd41	blood
37	chr9:101903600-101912200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:101903600-101915000	Strong transcription	HSMMtube	muscle
39	chr9:101903600-101915200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:101903800-101909800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:101903800-101911400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:101903800-101911600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:101903800-101912000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr9:101903800-101913000	Strong transcription	Adipose Nuclei	Adipose
45	chr9:101904000-101910800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:101904000-101911800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr9:101904000-101911800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:101904000-101912200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:101904000-101912200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr9:101904000-101912400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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