Variant report

Variant	rs13131868
Chromosome Location	chr4:16353313-16353314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16258640..16260295-chr4:16352186..16354704,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10002625	0.94[CEU][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10516298	1.00[YRI][hapmap]
rs10939659	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10939661	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11946067	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13102329	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13109787	0.84[ASN][1000 genomes]
rs13110673	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13111956	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13120292	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13121695	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13132621	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16893143	1.00[YRI][hapmap]
rs16893144	1.00[YRI][hapmap]
rs16893147	1.00[YRI][hapmap]
rs16893158	1.00[YRI][hapmap]
rs16893287	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34019415	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34274223	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34880816	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35281534	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35892656	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36104258	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4698139	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4698140	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4698142	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4698468	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4698480	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs7688779	0.94[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9994269	0.94[CEU][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv537048	chr4:16226406-16375787	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1002051	chr4:16335379-16363909	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv999436	chr4:16335379-16375164	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv432582	chr4:16335379-16379580	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv593779	chr4:16336013-16375164	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1000404	chr4:16338191-16363909	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1000106	chr4:16338191-16375164	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1006449	chr4:16338191-16412544	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1014580	chr4:16339728-16363909	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1005625	chr4:16339728-16375164	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1004586	chr4:16341873-16375164	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv517721	chr4:16350539-16365848	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13131868	NCAPG	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16351400-16354000	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr4:16352200-16353800	Enhancers	Brain Germinal Matrix	brain
3	chr4:16352600-16355000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:16352800-16353800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:16352800-16353800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:16352800-16353800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:16352800-16353800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:16352800-16353800	Enhancers	Fetal Brain Female	brain
9	chr4:16353000-16353600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:16353000-16353800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:16353000-16353800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:16353000-16353800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:16353000-16353800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:16353000-16353800	Enhancers	Brain Cingulate Gyrus	brain
15	chr4:16353200-16353400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:16353200-16353800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:16353200-16353800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:16353200-16353800	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links