Variant report

Variant	rs162278
Chromosome Location	chr19:53030170-53030171
allele	A/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	ELF1	chr19:53030076-53031232	GM12878	blood:	n/a	chr19:53030923-53030932 chr19:53030922-53030933 chr19:53030402-53030414 chr19:53030922-53030933 chr19:53030924-53030933
2	TCF3	chr19:53030141-53030391	GM12878	blood:	n/a	n/a
3	ELF1	chr19:53030148-53031258	SK-N-SH	brain:	n/a	chr19:53030923-53030932 chr19:53030922-53030933 chr19:53030402-53030414 chr19:53030922-53030933 chr19:53030924-53030933
4	POLR2A	chr19:53030159-53030621	GM12892	blood:	n/a	n/a
5	CBX3	chr19:53030053-53031085	K562	blood:	n/a	n/a
6	MTA3	chr19:53030098-53030561	GM12878	blood:	n/a	n/a
7	ELF1	chr19:53029926-53031661	GM12878	blood:	n/a	chr19:53030923-53030932 chr19:53030922-53030933 chr19:53030402-53030414 chr19:53030922-53030933 chr19:53030924-53030933
8	POLR2A	chr19:53030162-53030667	GM12878	blood:	n/a	n/a
9	RCOR1	chr19:53030055-53031984	IMR90	lung:	n/a	n/a
10	EGR1	chr19:53030135-53031250	HCT-116	colon:	n/a	chr19:53030403-53030418 chr19:53030404-53030417 chr19:53030405-53030414 chr19:53030856-53030866 chr19:53030403-53030417 chr19:53030405-53030415 chr19:53030404-53030417 chr19:53030858-53030872 chr19:53030404-53030417 chr19:53030855-53030865 chr19:53030401-53030415 chr19:53030404-53030414 chr19:53030404-53030417
11	ELF1	chr19:53029969-53031182	MCF-7	breast:	n/a	chr19:53030923-53030932 chr19:53030922-53030933 chr19:53030402-53030414 chr19:53030922-53030933 chr19:53030924-53030933
12	POLR2A	chr19:53030114-53031610	HL-60	blood:	n/a	n/a
13	MAX	chr19:53030159-53031179	SK-N-SH	brain:	n/a	chr19:53030956-53030965 chr19:53030855-53030865
14	POLR2A	chr19:53030082-53030173	GM12878	blood:	n/a	n/a
15	REST	chr19:53030137-53031519	H1-neurons	neurons:	n/a	chr19:53031361-53031374
16	EGR1	chr19:53030151-53031062	K562	blood:	n/a	chr19:53030403-53030418 chr19:53030404-53030417 chr19:53030405-53030414 chr19:53030856-53030866 chr19:53030403-53030417 chr19:53030405-53030415 chr19:53030404-53030417 chr19:53030858-53030872 chr19:53030404-53030417 chr19:53030855-53030865 chr19:53030401-53030415 chr19:53030404-53030414 chr19:53030404-53030417
17	ELF1	chr19:53030051-53031241	MCF-7	breast:	n/a	chr19:53030923-53030932 chr19:53030922-53030933 chr19:53030402-53030414 chr19:53030922-53030933 chr19:53030924-53030933
18	HEY1	chr19:53030127-53031218	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:53030095-53032548	GM12878	blood:	n/a	n/a
20	EGR1	chr19:53030113-53030675	MCF-7	breast:	n/a	chr19:53030403-53030418 chr19:53030404-53030417 chr19:53030405-53030414 chr19:53030403-53030417 chr19:53030405-53030415 chr19:53030404-53030417 chr19:53030404-53030417 chr19:53030401-53030415 chr19:53030404-53030414 chr19:53030404-53030417
21	POLR2A	chr19:53030037-53031648	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:53030098-53031524	HepG2	liver:	n/a	n/a
23	CTCF	chr19:53030080-53031679	SK-N-SH	brain:	n/a	chr19:53030482-53030491
24	POLR2A	chr19:53030165-53030645	GM12892	blood:	n/a	n/a
25	EGR1	chr19:53030117-53030596	H1-hESC	embryonic stem cell:	n/a	chr19:53030403-53030418 chr19:53030404-53030417 chr19:53030405-53030414 chr19:53030403-53030417 chr19:53030405-53030415 chr19:53030404-53030417 chr19:53030404-53030417 chr19:53030401-53030415 chr19:53030404-53030414 chr19:53030404-53030417
26	POLR2A	chr19:53030086-53031726	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:53024234..53025826-chr19:53029049..53030597,2	MCF-7	breast:
2	chr19:53029127..53032188-chr19:53072538..53075129,3	K562	blood:
3	chr19:53029450..53032188-chr19:53072538..53074123,2	K562	blood:
4	chr19:53029459..53032258-chr19:53036873..53039549,6	MCF-7	breast:

Variant related genes	Relation type
ZNF808	TF binding region
ENSG00000167562	Chromatin interaction
ENSG00000198482	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11668903	0.80[ASN][1000 genomes]
rs12462347	0.88[EUR][1000 genomes]
rs12463002	0.84[EUR][1000 genomes]
rs12974840	0.85[EUR][1000 genomes]
rs12982862	0.82[EUR][1000 genomes]
rs162277	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1676153	0.81[EUR][1000 genomes]
rs2608522	0.90[EUR][1000 genomes]
rs2608527	0.82[EUR][1000 genomes]
rs2633502	0.83[EUR][1000 genomes]
rs2633513	0.81[EUR][1000 genomes]
rs2868688	0.85[ASN][1000 genomes]
rs2925976	0.83[EUR][1000 genomes]
rs326440	0.82[EUR][1000 genomes]
rs326441	0.82[EUR][1000 genomes]
rs326447	0.81[EUR][1000 genomes]
rs326448	0.81[EUR][1000 genomes]
rs326449	0.80[EUR][1000 genomes]
rs326458	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34222822	0.87[EUR][1000 genomes]
rs36039960	0.87[EUR][1000 genomes]
rs368922	0.82[EUR][1000 genomes]
rs375267	0.82[EUR][1000 genomes]
rs376595	0.90[EUR][1000 genomes]
rs396663	0.87[EUR][1000 genomes]
rs400709	0.89[EUR][1000 genomes]
rs402737	0.82[EUR][1000 genomes]
rs410046	0.92[EUR][1000 genomes]
rs413751	0.92[EUR][1000 genomes]
rs413814	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs417599	0.90[EUR][1000 genomes]
rs422195	0.89[EUR][1000 genomes]
rs429367	0.91[EUR][1000 genomes]
rs434709	0.91[EUR][1000 genomes]
rs434788	0.82[EUR][1000 genomes]
rs439618	0.89[EUR][1000 genomes]
rs440545	0.91[EUR][1000 genomes]
rs441549	0.82[EUR][1000 genomes]
rs441850	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs445500	0.91[EUR][1000 genomes]
rs449671	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802965	0.82[EUR][1000 genomes]
rs4802972	0.90[EUR][1000 genomes]
rs520958	0.80[EUR][1000 genomes]
rs521703	0.81[EUR][1000 genomes]
rs529698	0.83[EUR][1000 genomes]
rs532449	0.83[EUR][1000 genomes]
rs606914	0.81[EUR][1000 genomes]
rs607477	0.81[EUR][1000 genomes]
rs62119356	0.83[ASN][1000 genomes]
rs642493	0.81[EUR][1000 genomes]
rs653483	0.83[EUR][1000 genomes]
rs656541	0.84[EUR][1000 genomes]
rs668882	0.84[EUR][1000 genomes]
rs685200	0.83[EUR][1000 genomes]
rs688646	0.91[EUR][1000 genomes]
rs8101346	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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	4 gene(s)	inside rSNPs	diseases
13	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53022000-53030200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:53023600-53030200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:53023600-53030200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr19:53023600-53030200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:53025600-53030200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:53025800-53030200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr19:53026400-53030200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:53029200-53030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:53029400-53031200	Active TSS	Primary T cells from cord blood	blood
10	chr19:53029600-53030200	Enhancers	Fetal Brain Male	brain
11	chr19:53029600-53030200	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr19:53029600-53031400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:53029600-53032000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr19:53029600-53032000	Active TSS	HSMM	muscle
15	chr19:53029600-53032200	Active TSS	Colonic Mucosa	Colon
16	chr19:53029800-53030200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:53029800-53030400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:53030000-53030200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:53030000-53030200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:53030000-53030200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:53030000-53030200	Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr19:53030000-53030200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:53030000-53030200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr19:53030000-53030200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr19:53030000-53030200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:53030000-53030200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr19:53030000-53030200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr19:53030000-53030200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:53030000-53030200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:53030000-53030200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr19:53030000-53030200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr19:53030000-53030200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:53030000-53030200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:53030000-53030200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:53030000-53030200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:53030000-53030200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:53030000-53030200	Active TSS	Adipose Nuclei	Adipose
38	chr19:53030000-53030200	Active TSS	Liver	Liver
39	chr19:53030000-53030200	Active TSS	Duodenum Mucosa	Duodenum
40	chr19:53030000-53030200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr19:53030000-53030200	Active TSS	Fetal Brain Female	brain
42	chr19:53030000-53030200	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr19:53030000-53030200	Enhancers	Lung	lung
44	chr19:53030000-53030200	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr19:53030000-53030200	Active TSS	GM12878-XiMat	blood
46	chr19:53030000-53030200	Enhancers	HUVEC	blood vessel
47	chr19:53030000-53030200	Enhancers	K562	blood
48	chr19:53030000-53030400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr19:53030000-53030400	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr19:53030000-53030400	Flanking Active TSS	Primary B cells from peripheral blood	blood

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