Variant report

Variant	rs12675013
Chromosome Location	chr8:119120079-119120080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:119112265..119114853-chr8:119117703..119122505,4	K562	blood:
2	chr8:119118327..119120231-chr8:119121736..119124039,3	MCF-7	breast:
3	chr8:119117691..119120187-chr8:119121459..119124230,3	K562	blood:
4	chr8:119116728..119118979-chr8:119119696..119121253,2	MCF-7	breast:
5	chr8:119118049..119120187-chr8:119121459..119124230,2	K562	blood:

Variant related genes	Relation type
ENSG00000182197	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10755915	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10808492	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10808494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10955855	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10955856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12548404	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13270513	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1811528	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3757991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4876400	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876791	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6469721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6991511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6993268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7008536	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7010382	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7011384	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7014053	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7818011	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7835605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7835956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7837824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897828	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs897830	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1015380	chr8:118948652-119418389	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv539736	chr8:118948652-119418389	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv831441	chr8:119055370-119262970	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2752195	chr8:119058819-119139819	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv821660	chr8:119082062-119312183	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv891412	chr8:119107051-119139385	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12675013	SNTB1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119112200-119120800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:119112400-119120600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr8:119112400-119120600	Weak transcription	Placenta	Placenta
4	chr8:119112400-119120600	Weak transcription	Thymus	Thymus
5	chr8:119112400-119120800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr8:119113200-119120800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr8:119115600-119120800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:119117200-119120200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
9	chr8:119117200-119120200	Transcr. at gene 5' and 3'	NHEK	skin
10	chr8:119117200-119123000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr8:119117200-119123000	Transcr. at gene 5' and 3'	Osteobl	bone
12	chr8:119117400-119123000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr8:119117600-119121000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:119118200-119120200	Transcr. at gene 5' and 3'	Liver	Liver
15	chr8:119118200-119121800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:119118400-119120800	Active TSS	Duodenum Mucosa	Duodenum
17	chr8:119118600-119120200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr8:119118600-119120400	Flanking Active TSS	HMEC	breast
19	chr8:119118800-119120200	Flanking Active TSS	HUVEC	blood vessel
20	chr8:119118800-119120400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr8:119118800-119122000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:119118800-119124800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:119118800-119125000	Active TSS	Aorta	Aorta
24	chr8:119119000-119122000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:119119000-119124600	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr8:119119000-119125000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr8:119119200-119120200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr8:119119200-119120200	Flanking Active TSS	GM12878-XiMat	blood
29	chr8:119119200-119120600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr8:119119200-119121200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr8:119119400-119120200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:119119400-119120200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
33	chr8:119119400-119120200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr8:119119400-119120200	Flanking Active TSS	A549	lung
35	chr8:119119400-119120200	Transcr. at gene 5' and 3'	HSMM	muscle
36	chr8:119119400-119120400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr8:119119400-119120600	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr8:119119400-119121000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr8:119119400-119121000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr8:119119400-119121000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr8:119119400-119121000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr8:119119400-119121600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr8:119119400-119122000	Active TSS	Ovary	ovary
44	chr8:119119400-119122800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr8:119119400-119123000	Flanking Active TSS	Hela-S3	cervix
46	chr8:119119400-119123200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr8:119119400-119123200	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr8:119119600-119120200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr8:119119600-119120200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr8:119119600-119120200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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