Variant report

Variant	rs16968477
Chromosome Location	chr15:74662387-74662388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74660610..74662672-chr15:74905973..74908755,2	K562	blood:
2	chr15:74660902..74662781-chr15:74907796..74910319,2	K562	blood:
3	chr15:74661188..74664135-chr15:74906547..74909297,3	MCF-7	breast:
4	chr15:74661132..74663482-chr15:74724672..74726267,2	K562	blood:
5	chr15:74662112..74663737-chr15:74896911..74899028,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260919	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000138623	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12438594	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12898858	0.89[AFR][1000 genomes]
rs12916123	0.89[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1843090	0.89[ASW][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2073475	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28681535	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3825944	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3935523	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4077583	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4077584	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4077585	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41556118	0.89[AFR][1000 genomes]
rs4505257	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4555110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4598865	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58844886	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60636222	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6495096	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7167038	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7174179	0.89[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7180275	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7181947	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv904351	chr15:74638965-74697084	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904352	chr15:74638965-74715205	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16968477	NRG4	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74658600-74665800	Weak transcription	Pancreas	Pancrea
2	chr15:74658600-74666200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:74658800-74664000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:74658800-74665800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:74658800-74666000	Weak transcription	Esophagus	oesophagus
6	chr15:74658800-74666200	Weak transcription	Right Atrium	heart
7	chr15:74659400-74666200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:74659800-74665400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:74659800-74666000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:74660000-74665600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:74660200-74665600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:74660200-74665800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:74660400-74663000	Weak transcription	Hela-S3	cervix
14	chr15:74660400-74665400	Weak transcription	Spleen	Spleen
15	chr15:74660400-74665800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:74661600-74662400	Enhancers	K562	blood
17	chr15:74661800-74665800	Weak transcription	Fetal Heart	heart
18	chr15:74662000-74664600	Weak transcription	Placenta	Placenta
19	chr15:74662000-74665800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr15:74662200-74663800	Weak transcription	Osteobl	bone
21	chr15:74662200-74665800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:74662200-74665800	Weak transcription	Adipose Nuclei	Adipose
23	chr15:74662200-74666200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:74662200-74666200	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links