Variant report

Variant	rs2282072
Chromosome Location	chr9:16727446-16727447
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:52445126..52445753-chr9:16726910..16727745,2	Hela-S3	cervix:
2	chr3:20227400..20228150-chr9:16726744..16727510,2	Hela-S3	cervix:
3	chr6:3068763..3069618-chr9:16726993..16727675,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTLN-2	chr9:16727313-16727522	ENSG00000234779.1

Variant related genes	Relation type
ENSG00000272277	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000129810	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10116407	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10116469	1.00[CEU][hapmap]
rs10117034	0.82[EUR][1000 genomes]
rs10122736	0.86[CEU][hapmap]
rs10122827	0.86[CEU][hapmap];0.88[YRI][hapmap]
rs10123118	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs10738457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes]
rs10756810	0.83[EUR][1000 genomes]
rs10810595	0.82[CEU][hapmap]
rs10810599	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10810600	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10810602	0.83[EUR][1000 genomes]
rs10810610	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10810614	0.84[EUR][1000 genomes]
rs10810615	0.83[EUR][1000 genomes]
rs10810617	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10810622	0.82[EUR][1000 genomes]
rs10962543	0.87[CEU][hapmap]
rs10962556	0.89[EUR][1000 genomes]
rs10962569	1.00[CEU][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs10962576	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs10962592	1.00[CEU][hapmap]
rs12238070	0.84[EUR][1000 genomes]
rs12341542	1.00[CEU][hapmap]
rs12344698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs12375507	0.87[CEU][hapmap]
rs12377846	0.85[CEU][hapmap]
rs1337386	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1361073	1.00[CEU][hapmap]
rs1856132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1999214	0.89[EUR][1000 genomes]
rs2039185	1.00[CEU][hapmap]
rs2150089	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs28626673	0.84[EUR][1000 genomes]
rs5016914	0.90[EUR][1000 genomes]
rs7024466	0.83[CHB][hapmap];0.88[YRI][hapmap]
rs7024720	0.80[EUR][1000 genomes]
rs73419969	0.89[EUR][1000 genomes]
rs7855044	0.84[EUR][1000 genomes]
rs7862734	1.00[CEU][hapmap];0.88[EUR][1000 genomes]

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:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16724400-16729800	Active TSS	Ovary	ovary
2	chr9:16724800-16728800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:16725200-16729400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:16726000-16727800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
5	chr9:16726000-16727800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr9:16726000-16728200	Active TSS	Colonic Mucosa	Colon
7	chr9:16726200-16727800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr9:16726200-16727800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr9:16726200-16728000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:16726200-16728000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:16726200-16728000	Bivalent/Poised TSS	Fetal Brain Male	brain
12	chr9:16726400-16727600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:16726400-16727600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr9:16726400-16727800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr9:16726400-16727800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr9:16726400-16727800	Active TSS	Fetal Muscle Leg	muscle
17	chr9:16726400-16727800	Active TSS	A549	lung
18	chr9:16726400-16727800	Active TSS	HSMM	muscle
19	chr9:16726400-16727800	Active TSS	NH-A	brain
20	chr9:16726400-16727800	Active TSS	NHDF-Ad	bronchial
21	chr9:16726400-16727800	Active TSS	NHLF	lung
22	chr9:16726400-16727800	Active TSS	Osteobl	bone
23	chr9:16726400-16728000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:16726400-16728000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:16726400-16728000	Active TSS	Colon Smooth Muscle	Colon
26	chr9:16726400-16728000	Active TSS	Fetal Lung	lung
27	chr9:16726400-16728200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr9:16726400-16728200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:16726400-16728400	Active TSS	HSMMtube	muscle
30	chr9:16726400-16729200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:16726600-16727600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:16726600-16727600	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr9:16726600-16727600	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr9:16726600-16727600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr9:16726600-16727600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:16726600-16727600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
37	chr9:16726600-16727600	Flanking Bivalent TSS/Enh	Liver	Liver
38	chr9:16726600-16727600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:16726600-16727600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
40	chr9:16726600-16727600	Active TSS	Hela-S3	cervix
41	chr9:16726600-16727800	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr9:16726600-16727800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr9:16726600-16727800	Active TSS	Brain Substantia Nigra	brain
44	chr9:16726600-16727800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr9:16726600-16727800	Active TSS	Placenta	Placenta
46	chr9:16726600-16727800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
47	chr9:16726600-16727800	Active TSS	HMEC	breast
48	chr9:16726600-16728000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:16726600-16728000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
50	chr9:16726600-16728000	Active TSS	Esophagus	oesophagus

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