Variant report

Variant	rs2275256
Chromosome Location	chr9:16625749-16625750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTLN-3	chr9:16625674-16625895	ENSG00000230694.1

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1003069	0.87[YRI][hapmap]
rs10756757	0.89[CEU][hapmap]
rs10756762	0.81[CEU][hapmap]
rs10810579	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10810580	0.83[YRI][hapmap]
rs10810581	0.83[YRI][hapmap]
rs10962519	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10962520	0.92[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11790341	0.89[CEU][hapmap];0.84[CHB][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13290470	0.80[CHD][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs1415471	0.84[CHD][hapmap]
rs1890074	0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2050617	0.84[CHB][hapmap]
rs4961727	0.84[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4961728	0.84[CHB][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7019299	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7023752	0.86[CEU][hapmap]
rs7033512	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7034582	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7043298	0.88[CEU][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7046245	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs943737	0.89[CEU][hapmap]
rs943738	0.89[CEU][hapmap]
rs9886876	0.85[CEU][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	nsv430000	chr9:16603483-16671045	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16611400-16626400	Weak transcription	Aorta	Aorta
2	chr9:16622400-16626200	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr9:16622400-16626600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr9:16622400-16628600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr9:16622400-16628600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:16622400-16628800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr9:16622600-16626400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:16622600-16628600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr9:16623200-16628000	Enhancers	Fetal Lung	lung
10	chr9:16623800-16626600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:16624000-16625800	Enhancers	HSMMtube	muscle
12	chr9:16624000-16628200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:16624200-16626400	Enhancers	Rectal Smooth Muscle	rectum
14	chr9:16624200-16626400	Enhancers	NHDF-Ad	bronchial
15	chr9:16624200-16626600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:16624200-16627600	Enhancers	Dnd41	blood
17	chr9:16624200-16629000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:16624200-16629200	Enhancers	Fetal Stomach	stomach
19	chr9:16624200-16630400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:16624400-16626400	Enhancers	Stomach Smooth Muscle	stomach
21	chr9:16624400-16627800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:16624400-16628800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr9:16624600-16625800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:16624600-16628800	Enhancers	Fetal Kidney	kidney
25	chr9:16624800-16626000	Enhancers	A549	lung
26	chr9:16624800-16626000	Enhancers	Osteobl	bone
27	chr9:16624800-16626600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:16624800-16628600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr9:16624800-16628800	Enhancers	Fetal Thymus	thymus
30	chr9:16625000-16626600	Enhancers	HSMM	muscle
31	chr9:16625000-16626800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:16625000-16628400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:16625000-16630000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:16625200-16625800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:16625200-16625800	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr9:16625200-16626000	Flanking Active TSS	HUVEC	blood vessel
37	chr9:16625200-16626800	Flanking Active TSS	NHLF	lung
38	chr9:16625200-16627800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:16625400-16625800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:16625400-16625800	Flanking Active TSS	Ovary	ovary
41	chr9:16625400-16626800	Enhancers	Psoas Muscle	Psoas
42	chr9:16625400-16627200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:16625400-16627200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr9:16625400-16627400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr9:16625400-16627800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:16625600-16625800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:16625600-16625800	Active TSS	Adipose Nuclei	Adipose
48	chr9:16625600-16625800	Enhancers	Colon Smooth Muscle	Colon
49	chr9:16625600-16625800	Enhancers	Fetal Brain Male	brain
50	chr9:16625600-16625800	Enhancers	Right Atrium	heart

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