Variant report

Variant	rs4461873
Chromosome Location	chr8:105584563-105584564
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:105583196..105585939-chr8:105600741..105602751,2	K562	blood:
2	chr8:105583573..105585685-chr8:105598077..105599877,2	K562	blood:

Variant related genes	Relation type
ENSG00000147650	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11987427	0.85[JPT][hapmap]
rs12541194	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12543329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12543736	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12544422	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12546843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12550349	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12674790	0.85[JPT][hapmap]
rs12680920	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12681417	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298840	0.89[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.80[LWK][hapmap];0.85[YRI][hapmap]
rs3750187	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap]
rs4474003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4609171	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510142	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66479713	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67341229	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67403507	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6988526	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72679139	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72679149	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73295140	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7813115	0.85[JPT][hapmap]
rs7814352	0.85[JPT][hapmap]
rs7823668	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7845549	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831417	chr8:105455814-105625608	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv508522	chr8:105532034-105614403	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2422460	chr8:105573376-105746329	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4461873	LRP12	cis	Skin Sun Exposed Lower leg	GTEx
rs4461873	LRP12	cis	parietal	SCAN
rs4461873	DPYS	cis	cerebellum	SCAN
rs4461873	LRP12	cis	lesional skin	skin_eQTL
rs4461873	LRP12	cis	cerebellum	SCAN
rs4461873	DCAF13	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105566200-105587200	Weak transcription	Left Ventricle	heart
2	chr8:105579800-105587600	Weak transcription	Fetal Heart	heart
3	chr8:105580400-105586200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr8:105580600-105585600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:105581600-105584800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
6	chr8:105581600-105590000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:105581600-105593000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:105581600-105598600	Weak transcription	Osteobl	bone
9	chr8:105583000-105584600	ZNF genes & repeats	GM12878-XiMat	blood
10	chr8:105583200-105584600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:105583200-105584600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr8:105583200-105585800	ZNF genes & repeats	Dnd41	blood
13	chr8:105583400-105584600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr8:105583400-105584600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr8:105583600-105584600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr8:105583600-105585800	ZNF genes & repeats	K562	blood
17	chr8:105583800-105584600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:105583800-105584600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:105584200-105585400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr8:105584200-105587200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:105584200-105587200	Weak transcription	Fetal Thymus	thymus
22	chr8:105584200-105587200	Weak transcription	Psoas Muscle	Psoas
23	chr8:105584200-105587200	Weak transcription	Thymus	Thymus
24	chr8:105584200-105588000	Weak transcription	Ovary	ovary
25	chr8:105584200-105600000	Weak transcription	Aorta	Aorta

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