Variant report

Variant	rs1004806
Chromosome Location	chr12:48589664-48589665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:48589640-48589790	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48587647..48589983-chr12:48590622..48592534,2	K562	blood:
2	chr12:48589603..48591970-chr12:48853785..48856420,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR10AD1-1	chr12:48588943-48591104	ucscGeneNc_uc001rvl_1

Variant related genes	Relation type
ENSG00000269514	TF binding region
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1004746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506276	0.87[EUR][1000 genomes]
rs10506277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506278	0.87[AMR][1000 genomes]
rs10506280	0.87[AMR][1000 genomes]
rs11830378	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11830864	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11833380	0.89[AMR][1000 genomes]
rs11837419	0.89[AMR][1000 genomes]
rs11837548	0.89[AMR][1000 genomes]
rs11837571	0.89[AMR][1000 genomes]
rs17122802	0.87[EUR][1000 genomes]
rs17122906	0.87[AMR][1000 genomes]
rs17224674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17224828	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17225198	0.89[AMR][1000 genomes]
rs17225261	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225366	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225751	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17226359	0.87[AMR][1000 genomes]
rs17226506	0.87[AMR][1000 genomes]
rs17226723	0.87[AMR][1000 genomes]
rs17823193	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17823313	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823415	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17823565	0.89[AMR][1000 genomes]
rs17824200	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17824705	0.87[AMR][1000 genomes]
rs17824989	0.87[AMR][1000 genomes]
rs17825013	0.87[AMR][1000 genomes]
rs2228501	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3936179	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4075914	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41291959	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41291961	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55638557	0.89[AMR][1000 genomes]
rs55654871	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55682541	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55707383	0.84[EUR][1000 genomes]
rs55752728	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55763362	0.87[AMR][1000 genomes]
rs55794326	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55854069	0.87[AMR][1000 genomes]
rs55886138	0.81[EUR][1000 genomes]
rs55890195	0.96[EUR][1000 genomes]
rs55894137	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55920439	0.87[AMR][1000 genomes]
rs55945889	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55953382	0.84[EUR][1000 genomes]
rs56049209	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56084718	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56110736	0.87[AMR][1000 genomes]
rs56116946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56187356	0.96[EUR][1000 genomes]
rs56205628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56271815	0.87[AMR][1000 genomes]
rs56288528	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56378908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56383074	0.87[AMR][1000 genomes]
rs56389692	0.87[AMR][1000 genomes]
rs56412095	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6580666	0.87[AMR][1000 genomes]
rs7138353	0.89[AMR][1000 genomes]
rs7297558	0.89[AMR][1000 genomes]
rs7301153	0.89[AMR][1000 genomes]
rs7301509	0.89[AMR][1000 genomes]
rs7307383	0.89[AMR][1000 genomes]
rs7307676	0.89[AMR][1000 genomes]
rs7307874	0.89[AMR][1000 genomes]
rs7310715	0.89[AMR][1000 genomes]
rs7310935	0.89[AMR][1000 genomes]
rs73304917	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74089155	0.96[EUR][1000 genomes]
rs74089159	0.85[EUR][1000 genomes]
rs74089163	0.85[EUR][1000 genomes]
rs751315	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs751316	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1004806	ZNF641	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48580000-48591000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:48583000-48590200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:48585400-48590800	Weak transcription	HMEC	breast
4	chr12:48585800-48589800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:48585800-48591400	Weak transcription	Esophagus	oesophagus
6	chr12:48587400-48590600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:48587400-48590800	Weak transcription	NHEK	skin
8	chr12:48587600-48590800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:48588200-48590000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:48588400-48590000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr12:48588400-48590800	Enhancers	A549	lung
12	chr12:48588800-48590000	Weak transcription	Fetal Kidney	kidney
13	chr12:48589000-48591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:48589200-48590200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:48589200-48590800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:48589200-48591000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:48589200-48591000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:48589200-48591000	Weak transcription	Fetal Heart	heart
19	chr12:48589200-48591000	Weak transcription	Hela-S3	cervix
20	chr12:48589200-48591000	Weak transcription	NHDF-Ad	bronchial
21	chr12:48589400-48589800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:48589400-48591000	Enhancers	Placenta	Placenta

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