Variant report

Variant	rs73044946
Chromosome Location	chr19:38892717-38892718
allele	A/C
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	POLR2A	chr19:38891621-38892723	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:38892623-38892722	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr19:38891235-38894621	A549	lung:	n/a	chr19:38893765-38893775 chr19:38893763-38893772 chr19:38893763-38893776 chr19:38893947-38893960 chr19:38893763-38893776 chr19:38893760-38893778 chr19:38893904-38893917 chr19:38893761-38893777 chr19:38893569-38893579
4	POLR2A	chr19:38887005-38894478	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr19:38886848-38892855	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:38892257-38892743	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr19:38890306-38894281	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38890926..38893595-chr19:38978170..38979921,2	K562	blood:
2	chr19:38864536..38866994-chr19:38891927..38895682,4	MCF-7	breast:
3	chr19:38886501..38890187-chr19:38891290..38894154,6	MCF-7	breast:
4	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
5	chr19:38891109..38897587-chr19:38900077..38906045,7	MCF-7	breast:
6	chr19:38810024..38812525-chr19:38892478..38895075,3	MCF-7	breast:
7	chr19:38891977..38893968-chr19:38915428..38917384,2	K562	blood:
8	chr19:38878160..38880019-chr19:38892423..38895031,2	MCF-7	breast:

Variant related genes	Relation type
FAM98C	TF binding region
ENSG00000099341	Chromatin interaction
ENSG00000171777	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000099337	Chromatin interaction
ENSG00000267473	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000188766	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11083454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11538289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2302228	1.00[EUR][1000 genomes]
rs3745955	0.80[EUR][1000 genomes]
rs3745963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3760884	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57753437	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59491640	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60780508	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508791	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508793	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257976	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043029	0.81[EUR][1000 genomes]
rs73043030	0.93[EUR][1000 genomes]
rs73043033	0.93[EUR][1000 genomes]
rs73043098	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73044905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044908	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044923	0.80[EUR][1000 genomes]
rs73044926	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044930	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73044948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8108440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38881000-38893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr19:38881000-38893200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:38881000-38893200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr19:38881000-38893200	Weak transcription	HSMMtube	muscle
5	chr19:38883600-38893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:38884800-38893200	Weak transcription	NH-A	brain
7	chr19:38885200-38893200	Weak transcription	HSMM	muscle
8	chr19:38885800-38893200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr19:38887000-38893200	Weak transcription	NHDF-Ad	bronchial
10	chr19:38887400-38893200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:38887400-38893200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:38887400-38893200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr19:38887400-38893200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:38887400-38893200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:38887400-38893200	Weak transcription	NHEK	skin
16	chr19:38887600-38893200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:38887600-38893200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:38887600-38893200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:38887600-38893200	Weak transcription	NHLF	lung
20	chr19:38887800-38893200	Weak transcription	Osteobl	bone
21	chr19:38888000-38893200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:38888000-38893200	Weak transcription	Right Atrium	heart
23	chr19:38891000-38893200	Enhancers	Placenta	Placenta
24	chr19:38891200-38893400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:38891400-38893200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:38891600-38893400	Enhancers	Stomach Mucosa	stomach
27	chr19:38892000-38893200	Weak transcription	A549	lung
28	chr19:38892000-38893200	Weak transcription	Hela-S3	cervix
29	chr19:38892000-38893200	Weak transcription	HUVEC	blood vessel
30	chr19:38892200-38893000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:38892200-38893200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:38892400-38893200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr19:38892400-38893200	Enhancers	Fetal Muscle Leg	muscle
34	chr19:38892400-38893200	Enhancers	K562	blood
35	chr19:38892600-38893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:38892600-38893200	Enhancers	Fetal Muscle Trunk	muscle
37	chr19:38892600-38893800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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