Variant report

Variant	rs1927631
Chromosome Location	chr9:16500789-16500790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10118463	0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs10118467	0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs10119184	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10123674	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10124550	0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs10124554	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10756756	0.89[CHB][hapmap]
rs10756760	0.85[CEU][hapmap]
rs10810571	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10810572	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10810573	0.97[ASN][1000 genomes]
rs10962454	0.86[ASN][1000 genomes]
rs10962456	0.85[ASN][1000 genomes]
rs10962457	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10962458	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10962459	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10962461	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10962463	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10962468	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10962470	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12115663	0.89[CEU][hapmap]
rs12156570	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12380362	0.90[CEU][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs16934786	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs17811225	0.84[CEU][hapmap]
rs35380246	0.84[ASN][1000 genomes]
rs36040975	0.83[ASN][1000 genomes]
rs66580280	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7020843	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7021958	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs7022474	1.00[YRI][hapmap]
rs7024707	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs7028447	0.94[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs7028666	0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs7035687	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7035706	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7037413	1.00[YRI][hapmap]
rs7041549	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7043485	0.84[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs7044580	0.95[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs7044870	0.94[YRI][hapmap]
rs73417442	0.83[AFR][1000 genomes]
rs7848343	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7848584	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7848696	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs7849139	0.89[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]

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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv892646	chr9:16476144-16514375	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS	lncRNA	n/a	inside rSNPs	diseases
6	nsv892647	chr9:16476144-16521534	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv466265	chr9:16484731-16516941	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
8	nsv613670	chr9:16484731-16516941	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1927631	TTC39B	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16471000-16504600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16483200-16513600	Weak transcription	Psoas Muscle	Psoas
3	chr9:16485000-16504800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr9:16485400-16505000	Weak transcription	HSMMtube	muscle
5	chr9:16485800-16505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:16488200-16504600	Weak transcription	Fetal Stomach	stomach
7	chr9:16488200-16505200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:16488800-16505000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:16489000-16504800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:16494000-16505000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:16494600-16504600	Weak transcription	Fetal Lung	lung
12	chr9:16495200-16509800	Weak transcription	Aorta	Aorta
13	chr9:16495800-16501800	Weak transcription	Ovary	ovary
14	chr9:16497200-16503000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:16497200-16504800	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:16499600-16502400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:16499800-16500800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:16499800-16502000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:16499800-16502200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:16499800-16502200	Enhancers	HMEC	breast
21	chr9:16499800-16502200	Enhancers	NHEK	skin
22	chr9:16499800-16502400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:16499800-16502400	Enhancers	NH-A	brain
24	chr9:16499800-16502800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:16500000-16501200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr9:16500000-16502200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:16500000-16502200	Enhancers	Hela-S3	cervix
28	chr9:16500000-16502200	Enhancers	NHLF	lung
29	chr9:16500000-16502400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:16500000-16502400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:16500000-16502400	Enhancers	HSMM	muscle
32	chr9:16500000-16502400	Enhancers	NHDF-Ad	bronchial
33	chr9:16500000-16505000	Enhancers	Osteobl	bone
34	chr9:16500000-16506400	Enhancers	HUVEC	blood vessel
35	chr9:16500200-16501600	Enhancers	A549	lung
36	chr9:16500200-16506600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:16500400-16501600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:16500400-16514000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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