Variant report

Variant	rs10738445
Chromosome Location	chr9:16680138-16680139
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10511624	0.83[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap]
rs10511625	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10733313	0.89[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs10733314	0.83[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs10733315	0.82[CEU][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs10733316	0.81[EUR][1000 genomes]
rs10738446	0.89[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs10738447	0.80[EUR][1000 genomes]
rs10738448	0.80[EUR][1000 genomes]
rs10738449	0.84[CEU][hapmap];0.83[CHB][hapmap];0.91[YRI][hapmap]
rs10756781	0.81[EUR][1000 genomes]
rs10756782	0.89[CEU][hapmap]
rs10756783	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs10756786	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs10756787	0.84[CEU][hapmap];0.87[YRI][hapmap]
rs10810590	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[ASN][1000 genomes]
rs10810591	0.89[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10810593	0.83[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs10962542	0.83[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs10962546	0.90[YRI][hapmap]
rs1337399	0.84[CEU][hapmap]
rs1888207	0.83[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs1888208	0.83[CEU][hapmap]
rs2026806	0.82[ASN][1000 genomes]
rs2297174	0.87[YRI][hapmap]
rs2297176	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs2383002	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2383004	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs3850444	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3850445	0.84[CEU][hapmap];0.87[YRI][hapmap]
rs3861709	0.89[CEU][hapmap]
rs3904778	0.84[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4111335	0.83[CEU][hapmap];0.83[YRI][hapmap]
rs4961732	0.94[CEU][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4961733	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4961734	0.94[CEU][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4961735	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4961736	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7028900	0.94[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription 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	10 gene(s)	inside rSNPs	diseases
8	nsv892648	chr9:16661092-16680901	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases
9	nsv892649	chr9:16677221-16761597	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1030598	chr9:16680138-16696510	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10738445	SH3GL2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16657600-16681400	Weak transcription	Psoas Muscle	Psoas
2	chr9:16665000-16704400	Weak transcription	Aorta	Aorta
3	chr9:16667200-16681000	Weak transcription	Fetal Stomach	stomach
4	chr9:16669000-16681400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:16671200-16681200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:16672000-16680800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:16672000-16681400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:16674200-16681800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:16675200-16682400	Weak transcription	A549	lung
10	chr9:16678800-16680200	Enhancers	Colon Smooth Muscle	Colon
11	chr9:16679200-16681200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:16679400-16680200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr9:16679400-16681600	Enhancers	HSMM	muscle
14	chr9:16679400-16681800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr9:16679600-16680200	Strong transcription	HUVEC	blood vessel
16	chr9:16679600-16681800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr9:16679600-16682000	Enhancers	Fetal Lung	lung
18	chr9:16679600-16683400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr9:16679600-16693600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr9:16679800-16680200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:16679800-16680600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:16679800-16681000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:16679800-16681000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr9:16679800-16681000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:16679800-16681400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:16679800-16689400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr9:16679800-16704000	Weak transcription	HSMMtube	muscle
28	chr9:16680000-16680200	Enhancers	NHLF	lung
29	chr9:16680000-16680600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:16680000-16680800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:16680000-16681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:16680000-16681000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:16680000-16681000	Weak transcription	Ovary	ovary
34	chr9:16680000-16681000	Enhancers	NHDF-Ad	bronchial
35	chr9:16680000-16681200	Weak transcription	NH-A	brain
36	chr9:16680000-16681400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:16680000-16681400	Weak transcription	Osteobl	bone
38	chr9:16680000-16681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:16680000-16681800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr9:16680000-16688800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr9:16680000-16688800	Weak transcription	Fetal Muscle Leg	muscle
42	chr9:16680000-16704600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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