Variant report

Variant	rs1571590
Chromosome Location	chr9:101883808-101883809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101881980..101884233-chr9:101923631..101926384,2	MCF-7	breast:
2	chr9:101877984..101880524-chr9:101882685..101887051,4	K562	blood:
3	chr9:101883649..101885819-chr9:101888623..101891146,2	MCF-7	breast:
4	chr9:101881851..101884905-chr9:101885246..101888669,5	K562	blood:
5	chr9:101882379..101885644-chr9:101887362..101889635,3	MCF-7	breast:
6	chr9:101882797..101885085-chr9:101894383..101896843,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1013186	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10283455	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]
rs10448292	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10733709	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10739779	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760668	0.94[EUR][1000 genomes]
rs10760669	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10760670	0.94[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs10760671	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10760672	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10760673	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10760674	0.83[AFR][1000 genomes]
rs10819634	0.84[EUR][1000 genomes]
rs10819635	0.83[CEU][hapmap];0.93[TSI][hapmap]
rs10819637	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819638	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10819639	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10988703	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988706	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10988714	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988716	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10988748	1.00[CHD][hapmap]
rs12345675	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12346650	0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs13286149	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571589	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs1590	0.89[CEU][hapmap]
rs1626340	0.81[EUR][1000 genomes]
rs1699413	0.86[EUR][1000 genomes]
rs2026811	0.94[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs334348	0.89[CEU][hapmap]
rs334349	0.89[CEU][hapmap]
rs334350	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334353	0.94[CEU][hapmap]
rs334354	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs334355	0.94[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs334356	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]
rs334357	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334358	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334362	0.85[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	0.80[EUR][1000 genomes]
rs385057	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401186	0.80[EUR][1000 genomes]
rs420549	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs44466	0.85[EUR][1000 genomes]
rs478061	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs597457	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6478972	0.94[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6478973	0.95[EUR][1000 genomes]
rs7031302	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7031309	0.89[EUR][1000 genomes]
rs7042852	0.94[CEU][hapmap]
rs7043624	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs7874221	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs789675	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868	0.84[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];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[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	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1571590	TGFBR1	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101868400-101896400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:101868600-101889800	Weak transcription	Ovary	ovary
3	chr9:101868600-101894400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:101869200-101884800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:101869800-101884800	Weak transcription	A549	lung
6	chr9:101870000-101908600	Weak transcription	Brain Germinal Matrix	brain
7	chr9:101870600-101889800	Weak transcription	NHLF	lung
8	chr9:101872600-101887800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:101874600-101889800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:101875600-101894600	Weak transcription	Spleen	Spleen
11	chr9:101876400-101889400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:101876600-101904200	Weak transcription	Liver	Liver
13	chr9:101877000-101884000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:101877000-101888200	Weak transcription	Osteobl	bone
15	chr9:101877000-101889400	Weak transcription	HSMMtube	muscle
16	chr9:101877200-101884400	Weak transcription	Aorta	Aorta
17	chr9:101877400-101887800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:101877400-101888200	Weak transcription	Right Ventricle	heart
19	chr9:101878000-101897400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr9:101878800-101891800	Weak transcription	Fetal Stomach	stomach
21	chr9:101878800-101892400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:101878800-101903200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:101879000-101884000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:101879000-101887400	Weak transcription	Fetal Brain Female	brain
25	chr9:101879400-101884000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:101879800-101884000	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:101879800-101888400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:101881400-101884200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:101881600-101884400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:101881600-101885200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr9:101881800-101884000	Weak transcription	Psoas Muscle	Psoas
32	chr9:101881800-101884400	Enhancers	Primary B cells from peripheral blood	blood
33	chr9:101881800-101885200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:101881800-101885800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:101881800-101887800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:101881800-101887800	Weak transcription	NHDF-Ad	bronchial
37	chr9:101882000-101884600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr9:101882000-101884600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:101882000-101885000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:101882000-101885200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr9:101882000-101885200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr9:101882000-101885200	Enhancers	Adipose Nuclei	Adipose
43	chr9:101882000-101888200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:101882000-101888200	Enhancers	Primary T cells from cord blood	blood
45	chr9:101882000-101892600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr9:101882000-101893400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr9:101882000-101893400	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr9:101882000-101895000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr9:101882200-101884200	Enhancers	Rectal Smooth Muscle	rectum
50	chr9:101882200-101884200	Weak transcription	Thymus	Thymus

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