Variant report

Variant	rs2290268
Chromosome Location	chr7:137010589-137010590
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHRM2-1	chr7:137010132-137011700	ENSG00000231114

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10227966	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10233933	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10241448	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10250267	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10255150	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10271620	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10282363	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1431090	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1431091	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1431093	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1431095	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs161093	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs161094	0.97[EUR][1000 genomes]
rs161095	0.96[EUR][1000 genomes]
rs320682	0.96[EUR][1000 genomes]
rs320715	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs320716	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs320719	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs320720	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs320721	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs320722	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs320723	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs320725	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs320726	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs321198	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs321200	0.96[EUR][1000 genomes]
rs322329	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807025	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv889240	chr7:136972027-137038092	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv889241	chr7:136976713-137038092	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv869820	chr7:136990386-137347718	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1027868	chr7:137004690-137311653	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv539134	chr7:137004690-137311653	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv889242	chr7:137005808-137081223	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290268	PTN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136991600-137013000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:136998200-137013000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:137001800-137016200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:137002000-137013000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:137002000-137020000	Weak transcription	Fetal Stomach	stomach
6	chr7:137004800-137016200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:137006000-137011200	Weak transcription	Brain Anterior Caudate	brain
8	chr7:137008000-137013000	Weak transcription	NH-A	brain
9	chr7:137009000-137011000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:137009000-137011200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr7:137009400-137014600	Enhancers	Brain Substantia Nigra	brain
12	chr7:137009600-137010600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr7:137009600-137011000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr7:137009600-137011000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr7:137009600-137011200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr7:137009800-137010600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr7:137009800-137011200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr7:137010000-137010800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:137010000-137012000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr7:137010000-137014200	Enhancers	Brain Cingulate Gyrus	brain
21	chr7:137010200-137010600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr7:137010200-137010800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr7:137010200-137011400	Enhancers	Brain Hippocampus Middle	brain
24	chr7:137010400-137010600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:137010400-137010800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:137010400-137012000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:137010400-137012200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr7:137010400-137014400	Enhancers	Brain Angular Gyrus	brain
29	chr7:137010400-137018200	Genic enhancers	Cortex derived primary cultured neurospheres	brain

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