Variant report

Variant	rs420549
Chromosome Location	chr9:101914873-101914874
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101914312..101916754-chr9:101918469..101920342,3	K562	blood:
2	chr9:101835256..101838008-chr9:101914700..101916909,2	K562	blood:
3	chr9:101911700..101915310-chr9:101917488..101920239,4	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1013186	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10283455	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]
rs10448292	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10733709	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10739779	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760668	0.86[EUR][1000 genomes]
rs10760669	0.87[EUR][1000 genomes]
rs10760670	0.94[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs10760671	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10760672	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10760673	1.00[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs10819635	0.83[CEU][hapmap];0.90[TSI][hapmap]
rs10819637	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819638	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10819639	0.94[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10988703	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988706	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10988714	0.83[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988716	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10988748	1.00[CHD][hapmap]
rs12345675	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12346650	0.90[TSI][hapmap]
rs13286149	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571589	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1571590	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]
rs1590	0.89[CEU][hapmap]
rs1626340	0.87[EUR][1000 genomes]
rs1699413	0.94[EUR][1000 genomes]
rs2026811	0.94[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs334348	0.89[CEU][hapmap]
rs334349	0.89[CEU][hapmap]
rs334350	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334353	0.94[CEU][hapmap]
rs334354	1.00[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs334355	0.94[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs334356	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]
rs334357	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334358	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334362	0.92[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	0.88[EUR][1000 genomes]
rs385057	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401186	0.88[EUR][1000 genomes]
rs44466	0.91[EUR][1000 genomes]
rs478061	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs597457	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6478972	0.94[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6478973	0.87[EUR][1000 genomes]
rs7031302	0.88[CEU][hapmap]
rs7031309	0.81[EUR][1000 genomes]
rs7042852	0.94[CEU][hapmap]
rs7043624	0.83[CEU][hapmap]
rs7874221	1.00[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs789675	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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
rs420549	TGFBR1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101892800-101921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:101897600-101915400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:101898000-101919400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:101900200-101915200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:101900800-101916800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:101902800-101915400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr9:101903000-101915200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr9:101903000-101921800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr9:101903200-101915000	Strong transcription	Osteobl	bone
10	chr9:101903400-101915400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:101903600-101915000	Strong transcription	HSMMtube	muscle
12	chr9:101903600-101915200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:101904000-101915800	Strong transcription	Placenta	Placenta
14	chr9:101904000-101916400	Strong transcription	Primary B cells from cord blood	blood
15	chr9:101904000-101917200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:101904600-101916200	Weak transcription	Fetal Intestine Small	intestine
17	chr9:101906200-101915000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:101906200-101915000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:101907200-101919800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:101907800-101916600	Weak transcription	Fetal Brain Male	brain
21	chr9:101908200-101922000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:101908400-101916600	Weak transcription	NHLF	lung
23	chr9:101908400-101918000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:101908600-101924600	Weak transcription	Gastric	stomach
25	chr9:101909000-101918600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:101909000-101920000	Weak transcription	HepG2	liver
27	chr9:101909200-101918000	Weak transcription	Fetal Stomach	stomach
28	chr9:101909600-101916200	Weak transcription	Brain Anterior Caudate	brain
29	chr9:101909800-101915800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:101910400-101920800	Weak transcription	K562	blood
31	chr9:101910600-101917600	Weak transcription	Ovary	ovary
32	chr9:101911000-101916400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr9:101911000-101920600	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:101911200-101918200	Weak transcription	Fetal Brain Female	brain
35	chr9:101911200-101921800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:101911200-101922000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:101911400-101916200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:101911400-101916600	Weak transcription	HUVEC	blood vessel
39	chr9:101911400-101925000	Weak transcription	Dnd41	blood
40	chr9:101911600-101916600	Weak transcription	GM12878-XiMat	blood
41	chr9:101911600-101917000	Weak transcription	Fetal Kidney	kidney
42	chr9:101911600-101922000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:101911800-101916200	Weak transcription	Colonic Mucosa	Colon
44	chr9:101911800-101916200	Weak transcription	Fetal Intestine Large	intestine
45	chr9:101911800-101916600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr9:101911800-101917400	Weak transcription	Fetal Lung	lung
47	chr9:101911800-101920600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:101912200-101916600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:101912200-101916600	Weak transcription	Brain Germinal Matrix	brain
50	chr9:101912400-101916200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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