Variant report

Variant	rs2840290
Chromosome Location	chr9:16733957-16733958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10738451	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10738452	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10738454	1.00[ASN][1000 genomes]
rs10738459	0.84[CHB][hapmap]
rs10756791	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756795	0.98[ASN][1000 genomes]
rs10756805	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs10756806	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs10756808	0.84[CHB][hapmap]
rs10810597	0.94[CEU][hapmap];0.84[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10810604	0.81[CEU][hapmap]
rs10810612	0.84[CHB][hapmap]
rs10962557	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13285058	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1330294	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1330296	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1330297	0.82[JPT][hapmap]
rs1330298	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1330302	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1361076	0.85[ASN][1000 genomes]
rs1411429	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs1411430	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537004	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs16934964	0.84[CHB][hapmap]
rs1854694	1.00[ASN][1000 genomes]
rs1888205	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1928849	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1970284	0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1970285	0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1980936	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2094781	0.84[CHB][hapmap]
rs2150090	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183408	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs2225327	0.82[ASN][1000 genomes]
rs2275255	0.84[CHB][hapmap]
rs3850446	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs3850447	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs3904154	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs4961739	0.92[ASN][1000 genomes]
rs4961740	0.92[ASN][1000 genomes]
rs4961742	0.92[ASN][1000 genomes]
rs4961744	0.92[ASN][1000 genomes]
rs4961750	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs4961751	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs5015536	0.84[CHB][hapmap]
rs5015537	0.84[CHB][hapmap]
rs5015539	0.84[CHB][hapmap]
rs5015540	0.84[CHB][hapmap]
rs6475074	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7034961	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7035732	0.81[ASN][1000 genomes]
rs7040406	0.96[ASN][1000 genomes]
rs7042146	0.87[ASN][1000 genomes]
rs73419968	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7853573	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7853764	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7853897	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7855308	0.92[ASN][1000 genomes]
rs7857721	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7857929	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7858709	0.81[ASN][1000 genomes]
rs7858712	0.81[ASN][1000 genomes]
rs7858914	0.81[ASN][1000 genomes]
rs7866023	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7868797	0.84[CHB][hapmap]
rs9987413	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9987476	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9987698	0.84[CHB][hapmap];0.82[JPT][hapmap]

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	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	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
9	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16728200-16744600	Weak transcription	Fetal Intestine Large	intestine
2	chr9:16728400-16736200	Weak transcription	HSMMtube	muscle
3	chr9:16728400-16743200	Weak transcription	Fetal Kidney	kidney
4	chr9:16728400-16744200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:16728800-16743400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:16729000-16734400	Weak transcription	NHLF	lung
7	chr9:16729000-16743200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:16729400-16744400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:16729600-16744200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:16729800-16735600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:16729800-16743400	Weak transcription	Osteobl	bone
12	chr9:16730000-16738200	Weak transcription	NH-A	brain
13	chr9:16730000-16744600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:16730200-16743400	Weak transcription	Fetal Stomach	stomach
15	chr9:16730200-16748200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:16730600-16735200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr9:16730600-16735400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr9:16730600-16735400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr9:16730600-16735400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr9:16730600-16744400	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:16730800-16734000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:16730800-16734400	Weak transcription	Ovary	ovary
23	chr9:16730800-16734600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:16731200-16735400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr9:16731200-16744600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:16732000-16735000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr9:16732000-16736000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:16732600-16734000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:16732600-16734200	Enhancers	NHEK	skin
30	chr9:16732800-16734600	Weak transcription	Fetal Lung	lung
31	chr9:16732800-16734800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:16733200-16734400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:16733200-16736000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:16733400-16743800	Weak transcription	HSMM	muscle
35	chr9:16733600-16734200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:16733800-16749200	Weak transcription	H1 Cell Line	embryonic stem cell

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