Variant report

Variant	rs12134197
Chromosome Location	chr1:221907587-221907588
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:221900354..221903760-chr1:221903849..221908437,4	MCF-7	breast:
2	chr1:221902184..221910150-chr1:221912477..221917248,16	K562	blood:
3	chr1:221859186..221861053-chr1:221907223..221909990,3	K562	blood:
4	chr1:221902783..221905534-chr1:221906000..221908483,2	K562	blood:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10779455	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863650	0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118830	1.00[ASN][1000 genomes]
rs11118832	1.00[ASN][1000 genomes]
rs11118849	1.00[ASN][1000 genomes]
rs11118851	1.00[ASN][1000 genomes]
rs11576121	1.00[ASN][1000 genomes]
rs12058360	1.00[ASN][1000 genomes]
rs12129426	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134869	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4275462	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs58058349	1.00[ASN][1000 genomes]
rs58969712	1.00[ASN][1000 genomes]
rs60950693	1.00[ASN][1000 genomes]
rs6679673	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689267	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693577	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67225019	1.00[ASN][1000 genomes]
rs72736551	1.00[ASN][1000 genomes]
rs72736552	1.00[ASN][1000 genomes]
rs72736557	1.00[ASN][1000 genomes]
rs72736561	1.00[ASN][1000 genomes]
rs72736562	1.00[ASN][1000 genomes]
rs72736563	1.00[ASN][1000 genomes]
rs72736571	1.00[ASN][1000 genomes]
rs7340042	1.00[ASN][1000 genomes]
rs7534227	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549374	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12134197	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221890800-221910200	Weak transcription	Lung	lung
2	chr1:221891800-221911000	Weak transcription	Gastric	stomach
3	chr1:221891800-221913000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:221893000-221913600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:221897200-221907800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:221897200-221914200	Weak transcription	Aorta	Aorta
7	chr1:221897400-221908800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:221897400-221913400	Weak transcription	HepG2	liver
9	chr1:221897600-221908000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:221897600-221910200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:221898600-221913600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:221899400-221912400	Weak transcription	Esophagus	oesophagus
13	chr1:221899600-221908000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:221899600-221912400	Weak transcription	Thymus	Thymus
15	chr1:221899800-221909600	Weak transcription	K562	blood
16	chr1:221899800-221910800	Weak transcription	NH-A	brain
17	chr1:221900200-221911200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:221901400-221913800	Weak transcription	Placenta	Placenta
19	chr1:221901800-221908400	Weak transcription	Small Intestine	intestine
20	chr1:221901800-221908600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:221901800-221913600	Weak transcription	Hela-S3	cervix
22	chr1:221901800-221913800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:221902400-221907800	Weak transcription	Primary B cells from cord blood	blood
24	chr1:221902400-221909400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:221902400-221910400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:221902600-221910000	Weak transcription	Primary T cells from cord blood	blood
27	chr1:221902600-221911200	Weak transcription	NHEK	skin
28	chr1:221903200-221908000	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:221903800-221907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:221903800-221907800	Weak transcription	Osteobl	bone
31	chr1:221903800-221908000	Weak transcription	Right Atrium	heart
32	chr1:221903800-221909400	Weak transcription	NHLF	lung
33	chr1:221903800-221909600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:221903800-221912400	Weak transcription	Fetal Intestine Small	intestine
35	chr1:221904000-221907600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:221904000-221908000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:221904000-221909200	Weak transcription	HSMMtube	muscle
38	chr1:221904000-221909600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:221904000-221909800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:221904000-221911200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:221904000-221911200	Weak transcription	Fetal Stomach	stomach
42	chr1:221904000-221912400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:221904000-221912600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:221904000-221913800	Weak transcription	Ovary	ovary
45	chr1:221904600-221907800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:221905200-221907600	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr1:221905400-221908200	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr1:221905600-221907600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr1:221905800-221909400	Weak transcription	Dnd41	blood
50	chr1:221905800-221913400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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