Variant report

Variant	rs401186
Chromosome Location	chr9:101925077-101925078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101762797..101765082-chr9:101923950..101926109,2	MCF-7	breast:
2	chr9:101920629..101922508-chr9:101923371..101925583,4	K562	blood:
3	chr9:101881980..101884233-chr9:101923631..101926384,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1013186	0.94[CEU][hapmap]
rs10283455	0.94[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs10733708	0.94[ASN][1000 genomes]
rs10733709	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10739778	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10739779	0.94[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs10760667	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10760668	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10760669	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10760670	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10760671	0.94[CEU][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10760672	0.94[CEU][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10760673	0.94[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10760674	0.81[AMR][1000 genomes]
rs10819634	0.88[AMR][1000 genomes]
rs10819635	0.94[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10819637	0.80[EUR][1000 genomes]
rs10819638	0.94[CEU][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10819639	0.89[CEU][hapmap]
rs10988706	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10988713	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs10988714	0.80[EUR][1000 genomes]
rs10988716	0.94[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10988723	0.87[AMR][1000 genomes]
rs12346650	0.94[ASW][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes]
rs12686783	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1571589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1571590	0.94[CEU][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs1590	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1626340	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699413	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1888223	0.81[ASN][1000 genomes]
rs1973518	0.83[ASN][1000 genomes]
rs2026811	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334348	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs334349	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs334350	0.89[EUR][1000 genomes]
rs334351	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs334353	0.81[ASW][hapmap];0.89[CEU][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs334354	0.94[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs334355	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334356	0.94[CEU][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs334357	0.94[CEU][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs334358	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs334362	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334363	0.83[ASN][1000 genomes]
rs334364	0.83[ASN][1000 genomes]
rs334365	0.98[ASN][1000 genomes]
rs334366	0.83[ASN][1000 genomes]
rs334367	0.83[ASN][1000 genomes]
rs334370	0.81[ASN][1000 genomes]
rs334371	0.97[ASN][1000 genomes]
rs367568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383496	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs385057	0.88[EUR][1000 genomes]
rs420549	0.94[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs44466	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs597457	0.94[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6478972	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478973	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7022989	0.85[CHB][hapmap]
rs7031302	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7031309	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042852	0.81[ASW][hapmap];0.89[CEU][hapmap];0.90[CHD][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7043624	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7874221	0.94[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs789675	0.89[EUR][1000 genomes]
rs868	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs401186	TGFBR1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101912600-101932200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:101914800-101927600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:101914800-101929800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:101915400-101927800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:101916000-101929600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:101922400-101930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:101922600-101930600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:101922800-101930000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:101922800-101932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:101923800-101925600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:101924600-101925200	Enhancers	Gastric	stomach
12	chr9:101924600-101925200	Enhancers	K562	blood
13	chr9:101924600-101925600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:101924600-101925600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:101924800-101925400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr9:101925000-101925200	Enhancers	Aorta	Aorta
17	chr9:101925000-101925200	Enhancers	Brain Cingulate Gyrus	brain
18	chr9:101925000-101925200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr9:101925000-101925200	Enhancers	Dnd41	blood
20	chr9:101925000-101925600	Enhancers	Primary T cells from cord blood	blood

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