Variant report

Variant	rs321198
Chromosome Location	chr7:137029838-137029839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTN-1	chr7:137029676-137029876	XLOC_006620
2	lnc-PTN-1	chr7:137029676-137029876	ENSG00000228031.2

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

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

rs_ID	r²[population]
rs10227966	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10233933	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10241448	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10250267	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10255150	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10271620	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10282363	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1431090	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1431091	0.87[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1431093	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1431095	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs161093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs161094	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs161095	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2290268	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs320682	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs320715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs320716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs320719	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs320720	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs320721	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs320722	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs320723	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs320725	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs320726	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs321200	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs322329	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7807025	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][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
rs321198	PTN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137028600-137030400	Weak transcription	Gastric	stomach
2	chr7:137028600-137030600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:137029000-137030000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
4	chr7:137029000-137030200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:137029000-137030400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr7:137029000-137030400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:137029000-137030400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:137029000-137030400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:137029000-137030800	Enhancers	Brain Hippocampus Middle	brain
10	chr7:137029200-137030200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr7:137029200-137030600	Weak transcription	Fetal Stomach	stomach
12	chr7:137029200-137031200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:137029200-137032400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:137029400-137030400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:137029800-137030600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links