Variant report

Variant	rs10028075
Chromosome Location	chr4:86967830-86967831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10001162	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10009993	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10023731	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1010778	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10856856	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11097091	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097092	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11934691	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502902	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12502934	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12512583	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12644938	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12644947	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs13103374	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13112959	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1436521	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1436527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469869	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1898249	0.81[GIH][hapmap]
rs2118044	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2589514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3775181	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775183	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4133139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4364253	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4482754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4487330	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4501213	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4640664	0.83[ASN][1000 genomes]
rs6531896	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840318	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7692676	0.98[ASN][1000 genomes]
rs9884770	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9995879	0.88[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9996208	0.91[ASN][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	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv998531	chr4:86966103-86980077	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv511259	chr4:86966327-86983232	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10028075	HNRPDL	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86916800-86985400	Weak transcription	Ovary	ovary
2	chr4:86936000-86975600	Weak transcription	Brain Germinal Matrix	brain
3	chr4:86936400-86990600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:86949200-86988600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:86955000-86985000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:86955200-86971000	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:86955200-87003800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:86956200-86969600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:86958200-86975600	Weak transcription	Fetal Brain Female	brain
10	chr4:86958400-86992600	Weak transcription	Fetal Kidney	kidney
11	chr4:86961200-86979400	Weak transcription	Fetal Stomach	stomach
12	chr4:86961200-86981000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:86963600-86974400	Weak transcription	Fetal Lung	lung
14	chr4:86963600-86988800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:86965200-86968000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:86965200-86968800	Weak transcription	NHDF-Ad	bronchial
17	chr4:86965200-86976200	Weak transcription	Brain Anterior Caudate	brain
18	chr4:86965200-86985800	Weak transcription	Adipose Nuclei	Adipose
19	chr4:86965200-86987000	Weak transcription	Brain Substantia Nigra	brain
20	chr4:86966800-86969000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:86967000-86968400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:86967200-86971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links