Variant report

Variant	rs73556542
Chromosome Location	chr19:44084683-44084684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 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	USF1	chr19:44084582-44084844	SK-N-SH_RA	brain:	n/a	n/a
5	CHD1	chr19:44084497-44084782	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:44084393-44084757	GM18505	blood:	n/a	n/a
7	POLR2A	chr19:44084286-44084888	GM18951	blood:	n/a	n/a
8	POLR2A	chr19:44084189-44084789	GM12878	blood:	n/a	n/a
9	ELF1	chr19:44084544-44084903	K562	blood:	n/a	n/a
10	YY1	chr19:44084448-44084718	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr19:44084649-44084915	HUVEC	blood vessel:	n/a	n/a
12	EP300	chr19:44084576-44084830	GM12878	blood:	n/a	n/a
13	JUND	chr19:44084276-44084997	H1-hESC	embryonic stem cell:	n/a	n/a
14	EP300	chr19:44084498-44084780	SK-N-SH_RA	brain:	n/a	n/a
15	EP300	chr19:44084449-44085003	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr19:44084347-44084690	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:44084350-44084722	GM12891	blood:	n/a	n/a
18	USF1	chr19:44084524-44084811	SK-N-SH_RA	brain:	n/a	n/a
19	POLR2A	chr19:44084313-44084989	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr19:44084347-44084950	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUND	chr19:44083900-44086327	SK-N-SH	brain:	n/a	chr19:44084081-44084088
22	POLR2A	chr19:44084355-44084789	SK-N-SH	brain:	n/a	n/a
23	MAX	chr19:44084505-44085148	H1-hESC	embryonic stem cell:	n/a	chr19:44084653-44084663
24	POLR2A	chr19:44084397-44084793	GM15510	blood:	n/a	n/a
25	POLR2A	chr19:44084417-44084788	K562	blood:	n/a	n/a
26	BHLHE40	chr19:44084585-44084785	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:44083975-44085128	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIX5	chr19:44084513-44084711	K562	blood:	n/a	n/a
29	GTF2F1	chr19:44084405-44084703	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF1	chr19:44084255-44085136	H1-hESC	embryonic stem cell:	n/a	n/a
31	JUND	chr19:44084526-44084809	H1-hESC	embryonic stem cell:	n/a	n/a
32	ELF1	chr19:44084323-44085103	GM12878	blood:	n/a	chr19:44084374-44084385
33	POLR2A	chr19:44084337-44085116	H1-hESC	embryonic stem cell:	n/a	n/a
34	CHD1	chr19:44084299-44085020	H1-hESC	embryonic stem cell:	n/a	n/a
35	BHLHE40	chr19:44084521-44084860	K562	blood:	n/a	n/a
36	EP300	chr19:44084474-44084852	GM12878	blood:	n/a	n/a
37	PML	chr19:44084067-44084920	GM12878	blood:	n/a	n/a
38	MAZ	chr19:44084555-44084702	K562	blood:	n/a	chr19:44084653-44084663
39	TBP	chr19:44084447-44084765	K562	blood:	n/a	n/a
40	EGR1	chr19:44084550-44084761	K562	blood:	n/a	chr19:44084647-44084662 chr19:44084652-44084662
41	EP300	chr19:44084490-44084829	H1-hESC	embryonic stem cell:	n/a	n/a
42	TBP	chr19:44084395-44085073	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:44084318-44084952	H1-hESC	embryonic stem cell:	n/a	n/a
44	ZBTB7A	chr19:44084640-44084805	K562	blood:	n/a	n/a
45	POLR2A	chr19:44084444-44084697	GM12878	blood:	n/a	n/a
46	TAF1	chr19:44084435-44084734	SK-N-SH	brain:	n/a	n/a
47	EGR1	chr19:44084638-44084819	GM12878	blood:	n/a	chr19:44084647-44084662 chr19:44084652-44084662
48	JUND	chr19:44084470-44084902	K562	blood:	n/a	n/a

No data

(count:6 , 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	chr19:44082536..44084852-chr19:44121728..44123814,2	K562	blood:

No data

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

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2307187	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682588	1.00[ASN][1000 genomes]
rs2854510	1.00[ASN][1000 genomes]
rs3213251	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213289	1.00[ASN][1000 genomes]
rs3213293	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213316	1.00[AFR][1000 genomes]
rs73554667	0.86[AFR][1000 genomes]
rs73554679	0.86[AFR][1000 genomes]
rs73556510	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73556512	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110767	0.86[AFR][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

No data

Chromatin state (count:119 , 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	chr19:44083800-44085200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr19:44083800-44085200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:44083800-44085200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:44083800-44085200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:44083800-44085200	Active TSS	Fetal Brain Female	brain
17	chr19:44083800-44085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:44083800-44085600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:44083800-44085800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr19:44083800-44085800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:44083800-44085800	Flanking Active TSS	Dnd41	blood
22	chr19:44084000-44084800	Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr19:44084000-44084800	Active TSS	NH-A	brain
24	chr19:44084000-44085000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr19:44084000-44085000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr19:44084000-44085000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:44084000-44085000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:44084000-44085200	Active TSS	Brain Angular Gyrus	brain
29	chr19:44084000-44085200	Active TSS	Brain Cingulate Gyrus	brain
30	chr19:44084000-44085200	Active TSS	Brain Hippocampus Middle	brain
31	chr19:44084000-44085200	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr19:44084000-44085200	Active TSS	Colonic Mucosa	Colon
33	chr19:44084000-44085200	Active TSS	Colon Smooth Muscle	Colon
34	chr19:44084000-44085200	Active TSS	Fetal Intestine Large	intestine
35	chr19:44084000-44085200	Active TSS	NHDF-Ad	bronchial
36	chr19:44084000-44085400	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr19:44084000-44085400	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr19:44084000-44085400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:44084000-44085400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:44084000-44085400	Active TSS	Fetal Kidney	kidney
41	chr19:44084000-44085600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:44084000-44085600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:44084000-44085600	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr19:44084000-44085600	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr19:44084000-44085600	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr19:44084000-44085600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr19:44084000-44085800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr19:44084000-44085800	Active TSS	NHLF	lung
49	chr19:44084200-44084800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:44084200-44085200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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