Variant report

Variant	rs1905953
Chromosome Location	chr4:175634795-175634796
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPGD-3	chr4:175634740-175634924	NONHSAT099324

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10008774	0.82[EUR][1000 genomes]
rs10022789	0.82[EUR][1000 genomes]
rs10032594	1.00[CHB][hapmap]
rs1352063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1485945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1485946	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17298140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298154	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363787	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1905954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087010	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2332939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695955	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[YRI][hapmap]
rs4695956	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[YRI][hapmap]
rs55780848	0.82[EUR][1000 genomes]
rs59690175	0.82[EUR][1000 genomes]
rs60210770	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61258069	0.82[EUR][1000 genomes]
rs72706187	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1018390	chr4:175475505-175969742	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv880584	chr4:175505749-175644689	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175633800-175635400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:175634200-175635200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr4:175634200-175635400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:175634200-175635400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr4:175634200-175635400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr4:175634200-175635400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:175634200-175635400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr4:175634200-175635600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:175634400-175635000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:175634400-175635200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:175634400-175635200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr4:175634400-175635200	Enhancers	Rectal Smooth Muscle	rectum
13	chr4:175634400-175635400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr4:175634400-175635400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:175634400-175635600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:175634600-175635000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:175634600-175635000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr4:175634600-175635200	Active TSS	Brain Anterior Caudate	brain
19	chr4:175634600-175635400	Flanking Active TSS	A549	lung
20	chr4:175634600-175636200	Enhancers	K562	blood

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