Variant report

Variant	rs13112959
Chromosome Location	chr4:86998264-86998265
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86996153..86999257-chr4:86999314..87002749,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10001162	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10002407	0.85[ASN][1000 genomes]
rs10009993	0.90[GIH][hapmap]
rs10023731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10027225	0.96[ASN][1000 genomes]
rs10028075	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]
rs10031752	0.88[ASN][1000 genomes]
rs1010778	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11097091	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11097092	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11929863	0.89[ASN][1000 genomes]
rs11934691	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12502902	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12502934	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644938	0.89[EUR][1000 genomes]
rs12644947	0.90[GIH][hapmap]
rs13103374	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13353771	0.91[ASN][1000 genomes]
rs1436521	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1436527	0.80[EUR][1000 genomes]
rs1469869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1898248	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1898249	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1946733	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2118044	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282596	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2282597	0.85[ASN][1000 genomes]
rs2282598	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2589506	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2589515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2589516	0.89[ASN][1000 genomes]
rs28485608	0.95[ASN][1000 genomes]
rs28865277	0.85[ASN][1000 genomes]
rs34998174	0.96[ASN][1000 genomes]
rs35823399	0.92[ASN][1000 genomes]
rs3775167	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3775170	0.85[ASN][1000 genomes]
rs3775181	1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs3775182	0.86[CHD][hapmap]
rs3775183	1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs3775184	0.91[ASN][1000 genomes]
rs3775187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4364253	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4482754	1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4487330	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4501213	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6531896	0.89[EUR][1000 genomes]
rs6810413	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6822410	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6840318	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9307015	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs958	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9884282	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[ASN][1000 genomes]
rs9884770	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9995879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv2760917	chr4:86975062-87000221	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1006616	chr4:86976082-86999794	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1000186	chr4:86976082-87000209	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv594761	chr4:86976413-87018488	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2754254	chr4:86979147-87108510	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv879521	chr4:86979927-87165758	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13112959	HNRPDL	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86955200-87003800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:86971800-87003800	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:86975200-87003600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:86976400-87000200	Weak transcription	Fetal Brain Female	brain
5	chr4:86977400-87003800	Weak transcription	Brain Anterior Caudate	brain
6	chr4:86980000-87004000	Weak transcription	Fetal Stomach	stomach
7	chr4:86985800-87003600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:86985800-87004000	Weak transcription	Ovary	ovary
9	chr4:86989200-86998800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:86989200-87004000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:86997400-86999600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:86997400-87003800	Weak transcription	Brain Angular Gyrus	brain
13	chr4:86997600-87000800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:86997800-87000600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:86997800-87000800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:86997800-87003600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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