Variant report

Variant	rs73054871
Chromosome Location	chr19:52197425-52197426
allele	A/G
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	chr19:52197239-52197426	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:52196227-52197752	PFSK-1	brain:	n/a	n/a
3	ZNF263	chr19:52196510-52197745	HEK293-T-REx	kidney:	n/a	n/a
4	POLR2A	chr19:52197286-52197789	K562	blood:	n/a	n/a
5	POLR2A	chr19:52196716-52199082	K562	blood:	n/a	n/a
6	ZNF263	chr19:52196681-52197780	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52196159..52199511-chr19:52202868..52206043,4	K562	blood:

Variant related genes	Relation type
SPACA6P-AS	TF binding region
SPACA6P	TF binding region
ENSG00000182310	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11881781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167417	0.97[ASN][1000 genomes]
rs2167418	0.97[ASN][1000 genomes]
rs2864920	0.97[ASN][1000 genomes]
rs2864922	0.94[ASN][1000 genomes]
rs34467678	0.86[EUR][1000 genomes]
rs34738545	0.88[EUR][1000 genomes]
rs34764077	0.97[ASN][1000 genomes]
rs35627212	0.90[EUR][1000 genomes]
rs35653323	0.97[ASN][1000 genomes]
rs4802841	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107937	0.97[ASN][1000 genomes]
rs8109852	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	esv1843680	chr19:52131510-52211749	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
12	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	518 gene(s)	inside rSNPs	diseases
13	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
14	nsv9742	chr19:52187538-52221742	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	517 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52194200-52205400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52194600-52205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:52194600-52207000	Weak transcription	Psoas Muscle	Psoas
4	chr19:52194800-52198600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:52194800-52204600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:52194800-52205200	Weak transcription	Stomach Mucosa	stomach
7	chr19:52195000-52198000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:52195000-52198000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:52195000-52205600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:52195000-52205600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr19:52195000-52205800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:52195000-52205800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:52195200-52199000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:52195200-52205800	Weak transcription	Primary T cells from cord blood	blood
15	chr19:52195400-52197600	Weak transcription	HSMMtube	muscle
16	chr19:52195400-52201400	Weak transcription	Liver	Liver
17	chr19:52195400-52204600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:52195400-52207200	Weak transcription	Hela-S3	cervix
19	chr19:52195600-52198000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:52195600-52198000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:52195600-52198600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:52195600-52203200	Strong transcription	Fetal Intestine Small	intestine
23	chr19:52195600-52204600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:52195600-52204800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:52195800-52197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr19:52195800-52197600	Strong transcription	Lung	lung
27	chr19:52195800-52197800	Enhancers	Right Atrium	heart
28	chr19:52195800-52198000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:52195800-52198200	Genic enhancers	Placenta	Placenta
30	chr19:52195800-52198800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:52195800-52204600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:52196000-52197600	Weak transcription	HSMM	muscle
33	chr19:52196000-52198600	Genic enhancers	A549	lung
34	chr19:52196000-52198800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:52196200-52197600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:52196200-52197600	Genic enhancers	Colon Smooth Muscle	Colon
37	chr19:52196200-52197600	Genic enhancers	Fetal Stomach	stomach
38	chr19:52196200-52197800	Weak transcription	Brain Anterior Caudate	brain
39	chr19:52196200-52197800	Genic enhancers	Fetal Muscle Leg	muscle
40	chr19:52196200-52198200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr19:52196200-52204800	Weak transcription	Colonic Mucosa	Colon
42	chr19:52196200-52204800	Strong transcription	NHEK	skin
43	chr19:52196200-52205600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:52196200-52205600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:52196400-52198000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:52196400-52198000	Weak transcription	Fetal Heart	heart
47	chr19:52196400-52198600	Strong transcription	NH-A	brain
48	chr19:52196400-52199600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr19:52196400-52199600	Strong transcription	Gastric	stomach
50	chr19:52196400-52200000	Weak transcription	Brain Substantia Nigra	brain

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