Variant report

Variant	rs2891071
Chromosome Location	chr9:16540987-16540988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10756759	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs10962467	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs10962472	1.00[YRI][hapmap]
rs1952347	0.84[ASW][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2149157	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4961492	1.00[YRI][hapmap]
rs7866317	0.86[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1028923	chr9:16519711-16547863	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2891071	TTC39B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16525000-16551400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:16528000-16553200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:16528800-16551200	Weak transcription	Fetal Intestine Large	intestine
4	chr9:16531400-16541200	Weak transcription	Fetal Lung	lung
5	chr9:16531400-16551200	Weak transcription	Fetal Stomach	stomach
6	chr9:16533000-16541200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:16534000-16542600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:16536000-16541000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:16536000-16541000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:16536000-16552200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:16536200-16551600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:16537400-16541200	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:16540400-16542000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:16540400-16542600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:16540400-16542800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr9:16540600-16541000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:16540600-16541000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:16540600-16541600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:16540600-16541600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:16540600-16542400	Enhancers	NH-A	brain
21	chr9:16540600-16542800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr9:16540600-16543600	Enhancers	Primary T cells from cord blood	blood
23	chr9:16540800-16541000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:16540800-16541200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:16540800-16541200	Genic enhancers	Ovary	ovary
26	chr9:16540800-16541400	Enhancers	Fetal Muscle Leg	muscle
27	chr9:16540800-16541600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:16540800-16541600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:16540800-16541600	Enhancers	Fetal Thymus	thymus
30	chr9:16540800-16541600	Enhancers	Psoas Muscle	Psoas
31	chr9:16540800-16541800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:16540800-16542000	Enhancers	HSMMtube	muscle
33	chr9:16540800-16542000	Enhancers	NHDF-Ad	bronchial
34	chr9:16540800-16542200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:16540800-16542400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr9:16540800-16542600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr9:16540800-16542600	Enhancers	A549	lung
38	chr9:16540800-16542600	Enhancers	NHLF	lung
39	chr9:16540800-16542800	Enhancers	HSMM	muscle
40	chr9:16540800-16543400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:16540800-16543800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:16540800-16544400	Enhancers	Osteobl	bone

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