Variant report

Variant	rs304729
Chromosome Location	chr19:44084403-44084404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr19:44084363-44085079	H1-hESC	embryonic stem cell:	n/a	n/a
2	MTA3	chr19:44084133-44084734	GM12878	blood:	n/a	n/a
3	TAF1	chr19:44084179-44084780	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:44084393-44084757	GM18505	blood:	n/a	n/a
5	POLR2A	chr19:44084286-44084888	GM18951	blood:	n/a	n/a
6	POLR2A	chr19:44084189-44084789	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:44084352-44084678	GM12891	blood:	n/a	n/a
8	NFATC1	chr19:44084119-44084461	GM12878	blood:	n/a	n/a
9	JUND	chr19:44084276-44084997	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:44084347-44084690	GM12891	blood:	n/a	n/a
11	POLR2A	chr19:44084350-44084722	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:44084313-44084989	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:44084347-44084950	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUND	chr19:44083900-44086327	SK-N-SH	brain:	n/a	chr19:44084081-44084088
15	POLR2A	chr19:44084355-44084789	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr19:44084397-44084793	GM15510	blood:	n/a	n/a
17	POLR2A	chr19:44083975-44085128	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr19:44084255-44085136	H1-hESC	embryonic stem cell:	n/a	n/a
19	STAT5A	chr19:44084093-44084547	GM12878	blood:	n/a	chr19:44084394-44084406 chr19:44084272-44084284
20	ELF1	chr19:44084323-44085103	GM12878	blood:	n/a	chr19:44084374-44084385
21	POLR2A	chr19:44084337-44085116	H1-hESC	embryonic stem cell:	n/a	n/a
22	CHD1	chr19:44084299-44085020	H1-hESC	embryonic stem cell:	n/a	n/a
23	RUNX3	chr19:44084372-44084645	GM12878	blood:	n/a	n/a
24	PML	chr19:44084067-44084920	GM12878	blood:	n/a	n/a
25	TBP	chr19:44084395-44085073	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:44084318-44084952	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44082767..44086072-chr19:44097414..44100193,3	MCF-7	breast:
2	chr19:44083278..44085752-chr19:44098903..44101247,2	MCF-7	breast:
3	chr19:44082516..44084852-chr19:44122314..44123953,3	K562	blood:
4	chr19:44078955..44081902-chr19:44082644..44085623,4	MCF-7	breast:
5	chr19:44079920..44081896-chr19:44082367..44084716,3	K562	blood:
6	chr19:44079733..44081896-chr19:44082367..44084669,4	K562	blood:
7	chr19:44082536..44084852-chr19:44121728..44123814,2	K562	blood:

No data

Variant related genes	Relation type
PINLYP	TF binding region
XRCC1	TF binding region
ENSG00000131116	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000234465	Chromatin interaction
ENSG00000226763	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11407	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2021092	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs25484	0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2599442	0.89[YRI][hapmap]
rs2599459	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2599464	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682552	0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682560	0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682562	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682587	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2682588	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2854495	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854496	0.80[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2854497	0.80[YRI][hapmap]
rs2854498	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854502	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2854505	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2854510	0.80[CEU][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes]
rs304730	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3213283	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3213285	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3213289	0.85[EUR][1000 genomes]
rs3213332	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3213370	0.87[EUR][1000 genomes]
rs939460	0.80[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][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	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs304729	ZNF575	cis	Skin Sun Exposed Lower leg	GTEx
rs304729	ZNF575	cis	Nerve Tibial	GTEx
rs304729	PHLDB3	cis	lesional skin	skin_eQTL
rs304729	PHLDB3	cis	normal skin	skin_eQTL
rs304729	ZNF575	cis	Artery Tibial	GTEx
rs304729	ZNF575	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44079800-44085400	Weak transcription	Gastric	stomach
2	chr19:44079800-44098200	Weak transcription	Small Intestine	intestine
3	chr19:44080400-44090200	Weak transcription	HSMM	muscle
4	chr19:44080600-44090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:44080600-44095600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:44080800-44088400	Weak transcription	A549	lung
7	chr19:44081000-44085200	Weak transcription	Pancreas	Pancrea
8	chr19:44081400-44090200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:44081400-44090200	Weak transcription	NHEK	skin
10	chr19:44081600-44090600	Weak transcription	HMEC	breast
11	chr19:44083000-44087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:44083800-44084600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:44083800-44085200	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr19:44083800-44085200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:44083800-44085200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:44083800-44085200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:44083800-44085200	Active TSS	Fetal Brain Female	brain
18	chr19:44083800-44085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:44083800-44085600	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr19:44083800-44085800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:44083800-44085800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:44083800-44085800	Flanking Active TSS	Dnd41	blood
23	chr19:44084000-44084600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:44084000-44084600	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr19:44084000-44084600	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr19:44084000-44084600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr19:44084000-44084600	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr19:44084000-44084600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr19:44084000-44084600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:44084000-44084600	Flanking Active TSS	Brain Germinal Matrix	brain
31	chr19:44084000-44084600	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr19:44084000-44084600	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr19:44084000-44084600	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr19:44084000-44084800	Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr19:44084000-44084800	Active TSS	NH-A	brain
36	chr19:44084000-44085000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr19:44084000-44085000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr19:44084000-44085000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:44084000-44085000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:44084000-44085200	Active TSS	Brain Angular Gyrus	brain
41	chr19:44084000-44085200	Active TSS	Brain Cingulate Gyrus	brain
42	chr19:44084000-44085200	Active TSS	Brain Hippocampus Middle	brain
43	chr19:44084000-44085200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr19:44084000-44085200	Active TSS	Colonic Mucosa	Colon
45	chr19:44084000-44085200	Active TSS	Colon Smooth Muscle	Colon
46	chr19:44084000-44085200	Active TSS	Fetal Intestine Large	intestine
47	chr19:44084000-44085200	Active TSS	NHDF-Ad	bronchial
48	chr19:44084000-44085400	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr19:44084000-44085400	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr19:44084000-44085400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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