Variant report

Variant	rs1414148
Chromosome Location	chr9:117963612-117963613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10739433	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739434	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759760	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759762	0.83[CHB][hapmap]
rs10817722	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10817728	0.91[CHB][hapmap]
rs1271449	0.82[MEX][hapmap]
rs1335340	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1335343	0.86[JPT][hapmap]
rs1335344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335345	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335354	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1335355	0.86[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1335356	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1335360	0.91[CHB][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1360823	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1414138	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1414150	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1537731	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537733	0.86[ASW][hapmap];0.91[CHB][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap]
rs1537734	0.91[CHB][hapmap]
rs1544126	0.80[AFR][1000 genomes]
rs1591421	0.82[JPT][hapmap]
rs1591422	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1591423	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4978625	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4978626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979508	0.91[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4979511	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6478147	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6478150	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478151	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6478152	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027442	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7027882	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7031000	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7043594	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7043679	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7044001	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7044556	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045288	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7045508	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045599	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7357796	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7470092	0.86[EUR][1000 genomes]
rs945258	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893769	chr9:117936903-117985886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1414148	TNC	cis	lymphoblastoid	seeQTL
rs1414148	TXN	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117930000-117964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:117955600-117969000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:117959400-117968600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:117960600-117964400	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:117960600-117964600	Weak transcription	NH-A	brain
6	chr9:117960600-117967400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:117960600-117969000	Weak transcription	Spleen	Spleen
8	chr9:117960800-117964600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:117960800-117964600	Weak transcription	Fetal Stomach	stomach
10	chr9:117960800-117965000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:117960800-117968800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:117960800-117969400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:117960800-117975800	Weak transcription	Fetal Kidney	kidney
14	chr9:117961600-117965600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:117962200-117972600	Enhancers	NHDF-Ad	bronchial
16	chr9:117962400-117964600	Weak transcription	Fetal Lung	lung
17	chr9:117962400-117966400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:117962400-117972400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:117962600-117963800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr9:117962600-117963800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:117962800-117963800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:117963000-117963800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:117963000-117964000	Enhancers	HMEC	breast
24	chr9:117963000-117965600	Enhancers	Adipose Nuclei	Adipose
25	chr9:117963000-117972600	Enhancers	NHEK	skin
26	chr9:117963000-117972600	Enhancers	Osteobl	bone
27	chr9:117963000-117977200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:117963200-117964200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:117963200-117964200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:117963200-117969800	Enhancers	NHLF	lung
31	chr9:117963400-117963800	Enhancers	Psoas Muscle	Psoas
32	chr9:117963400-117964400	Weak transcription	Aorta	Aorta
33	chr9:117963600-117964400	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:117963600-117965200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:117963600-117967000	Weak transcription	HSMM	muscle
36	chr9:117963600-117969000	Weak transcription	Esophagus	oesophagus

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