Variant report

Variant	rs2153271
Chromosome Location	chr9:16864521-16864522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10283446	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10756822	0.84[ASN][1000 genomes]
rs10810648	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10810650	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10810652	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810655	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810657	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10962650	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10962668	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12345776	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12350739	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1339552	1.00[CEU][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1416742	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1890640	0.83[ASN][1000 genomes]
rs28498684	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36116821	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3927680	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4644350	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62541919	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7040151	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv892651	chr9:16816755-16869240	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv892652	chr9:16843128-16958312	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv892653	chr9:16848790-16895610	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	esv1814340	chr9:16851678-16865699	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Freckling	20585627	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2153271	CNTLN	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16855800-16864600	Weak transcription	Psoas Muscle	Psoas
2	chr9:16860800-16867800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:16862400-16864600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:16862400-16868000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:16863400-16864600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:16863400-16864600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:16863800-16864600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:16863800-16864600	Enhancers	Osteobl	bone
9	chr9:16864200-16864600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr9:16864200-16864600	Enhancers	Fetal Lung	lung
11	chr9:16864200-16864800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr9:16864200-16867600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:16864400-16864600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:16864400-16864600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:16864400-16864600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:16864400-16864600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:16864400-16864600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:16864400-16864600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:16864400-16864600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:16864400-16864600	Enhancers	Adipose Nuclei	Adipose
21	chr9:16864400-16864600	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr9:16864400-16864600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr9:16864400-16864800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:16864400-16864800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr9:16864400-16864800	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr9:16864400-16865000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr9:16864400-16865000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr9:16864400-16865000	Enhancers	Fetal Muscle Leg	muscle
29	chr9:16864400-16865000	Active TSS	Ovary	ovary
30	chr9:16864400-16865000	Flanking Active TSS	HSMMtube	muscle
31	chr9:16864400-16865200	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr9:16864400-16865200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr9:16864400-16865200	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr9:16864400-16865200	Flanking Active TSS	HSMM	muscle
35	chr9:16864400-16865200	Flanking Active TSS	NHLF	lung
36	chr9:16864400-16865400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:16864400-16865400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr9:16864400-16865400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:16864400-16865600	Enhancers	Fetal Stomach	stomach
40	chr9:16864400-16865600	Flanking Active TSS	NH-A	brain
41	chr9:16864400-16865800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:16864400-16865800	Enhancers	A549	lung
43	chr9:16864400-16866000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr9:16864400-16867800	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr9:16864400-16867800	Enhancers	NHDF-Ad	bronchial
46	chr9:16864400-16868000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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