Variant report

Variant	rs10283455
Chromosome Location	chr9:101905643-101905644
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	chr9:101899920..101901969-chr9:101905038..101907406,2	K562	blood:
2	chr9:101865858..101869567-chr9:101901452..101906002,4	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]
rs10448292	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];0.91[MEX][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];0.96[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	0.82[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];0.91[YRI][hapmap];0.81[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];0.88[YRI][hapmap];0.85[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	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12346650	0.93[TSI][hapmap]
rs13286149	0.85[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];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];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];0.96[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];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs334356	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]
rs334357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[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];1.00[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];0.91[MEX][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];0.96[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];0.96[TSI][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs789675	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];0.85[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.91[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
rs10283455	TGFBR1	cis	cerebellum	SCAN

Chromatin state (count:121 , 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	chr9:101888200-101907000	Weak transcription	HepG2	liver
3	chr9:101890000-101914200	Weak transcription	Pancreas	Pancrea
4	chr9:101890200-101907600	Weak transcription	Gastric	stomach
5	chr9:101890400-101908400	Weak transcription	Hela-S3	cervix
6	chr9:101890600-101907000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:101890600-101908800	Weak transcription	Right Ventricle	heart
8	chr9:101892600-101914200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:101892800-101905800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:101892800-101921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:101894200-101906800	Weak transcription	Fetal Kidney	kidney
12	chr9:101894200-101907600	Weak transcription	HUVEC	blood vessel
13	chr9:101895000-101907200	Weak transcription	Spleen	Spleen
14	chr9:101895000-101914200	Weak transcription	Esophagus	oesophagus
15	chr9:101897600-101907400	Weak transcription	HMEC	breast
16	chr9:101897600-101913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:101897600-101915400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:101897800-101906800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:101898000-101907000	Weak transcription	NHLF	lung
20	chr9:101898000-101907200	Weak transcription	Small Intestine	intestine
21	chr9:101898000-101907400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:101898000-101907400	Weak transcription	Brain Angular Gyrus	brain
23	chr9:101898000-101907400	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:101898000-101907400	Weak transcription	Brain Substantia Nigra	brain
25	chr9:101898000-101912200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:101898000-101919400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr9:101898200-101906000	Weak transcription	Fetal Brain Male	brain
28	chr9:101899000-101906800	Weak transcription	Fetal Thymus	thymus
29	chr9:101899000-101913000	Strong transcription	HSMM	muscle
30	chr9:101899400-101908000	Weak transcription	Colonic Mucosa	Colon
31	chr9:101899400-101913000	Weak transcription	Thymus	Thymus
32	chr9:101900000-101905800	Weak transcription	GM12878-XiMat	blood
33	chr9:101900200-101914800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr9:101900200-101915200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:101900800-101916800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:101901000-101905800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:101901200-101905800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr9:101901200-101908000	Weak transcription	Psoas Muscle	Psoas
39	chr9:101901800-101907000	Weak transcription	Ovary	ovary
40	chr9:101901800-101912000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:101902200-101906000	Strong transcription	NHEK	skin
42	chr9:101902200-101911200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:101902800-101914200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:101902800-101915400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr9:101903000-101911000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:101903000-101911800	Strong transcription	Fetal Muscle Leg	muscle
47	chr9:101903000-101915200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr9:101903000-101921800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr9:101903200-101905800	Weak transcription	Fetal Heart	heart
50	chr9:101903200-101906000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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