Variant report

Variant	rs13275942
Chromosome Location	chr8:118921721-118921722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	8:118911988-118922970..8:119208477-119211356	GM12878	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10110572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10808489	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[EUR][1000 genomes]
rs13251971	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13252084	0.83[JPT][hapmap]
rs13266866	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.95[ASN][1000 genomes]
rs13280053	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4467961	0.90[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs4480148	0.86[JPT][hapmap]
rs4621831	0.83[JPT][hapmap]
rs4876769	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876770	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4876774	0.85[CHB][hapmap]
rs6469715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6981592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6990519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6997503	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7002023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7014561	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7814022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7841914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9692869	1.00[CEU][hapmap];0.89[GIH][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019636	chr8:118598433-118946091	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv539734	chr8:118598433-118946091	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv933516	chr8:118764605-119009093	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
5	nsv831440	chr8:118871930-119052269	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv891411	chr8:118891896-118942698	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032355	chr8:118896733-119003223	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv465785	chr8:118901928-118970300	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv612046	chr8:118901928-118970300	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13275942	EXT1	cis	parietal	SCAN
rs13275942	NOBOX	trans	multi-tissue	Pritchard

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118908800-118925800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr8:118909600-118922200	Weak transcription	Right Ventricle	heart
3	chr8:118909800-118923000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr8:118911400-118921800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:118912000-118925800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr8:118913000-118922000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:118913000-118922600	Weak transcription	Lung	lung
8	chr8:118913000-118923200	Weak transcription	Gastric	stomach
9	chr8:118913400-118922600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr8:118913400-118925600	Weak transcription	Colon Smooth Muscle	Colon
11	chr8:118915400-118922400	Weak transcription	Fetal Heart	heart
12	chr8:118915600-118922200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr8:118916200-118925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr8:118917800-118923200	Weak transcription	Esophagus	oesophagus
15	chr8:118918000-118923000	Weak transcription	Pancreas	Pancrea
16	chr8:118918400-118922200	Weak transcription	Ovary	ovary
17	chr8:118918600-118922600	Weak transcription	Fetal Brain Male	brain
18	chr8:118918800-118922600	Weak transcription	HSMMtube	muscle
19	chr8:118919000-118926800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr8:118919200-118933200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr8:118919400-118921800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr8:118919400-118922200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr8:118919400-118922200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr8:118919400-118922600	Weak transcription	HSMM	muscle
25	chr8:118919600-118922800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr8:118919800-118921800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr8:118919800-118921800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:118919800-118922000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr8:118919800-118922200	Weak transcription	Psoas Muscle	Psoas
30	chr8:118919800-118922200	Weak transcription	Right Atrium	heart
31	chr8:118919800-118922400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr8:118919800-118922400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr8:118919800-118922400	Weak transcription	HepG2	liver
34	chr8:118919800-118922600	Weak transcription	Aorta	Aorta
35	chr8:118919800-118922600	Weak transcription	Liver	Liver
36	chr8:118919800-118925800	Weak transcription	Small Intestine	intestine
37	chr8:118920000-118921800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:118920000-118921800	Weak transcription	NHLF	lung
39	chr8:118920000-118922200	Weak transcription	HUVEC	blood vessel
40	chr8:118921200-118926400	Enhancers	NHDF-Ad	bronchial
41	chr8:118921200-118926600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:118921400-118922400	Enhancers	A549	lung
43	chr8:118921400-118923800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr8:118921400-118924600	Enhancers	HMEC	breast
45	chr8:118921600-118922600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr8:118921600-118922600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr8:118921600-118922600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr8:118921600-118922600	Enhancers	Osteobl	bone
49	chr8:118921600-118924000	Enhancers	NHEK	skin
50	chr8:118921600-118924200	Enhancers	NH-A	brain

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