Variant report

Variant	rs73599602
Chromosome Location	chr19:36427163-36427164
allele	G/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	MTA3	chr19:36426767-36427296	GM12878	blood:	n/a	n/a
2	ZNF143	chr19:36426904-36427309	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZBTB7A	chr19:36426958-36427770	ECC-1	luminal epithelium:	n/a	chr19:36427222-36427229
4	CHD2	chr19:36427142-36427443	Hela-S3	cervix:	n/a	chr19:36427407-36427417
5	SIN3AK20	chr19:36427070-36427342	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr19:36427083-36427388	Hela-S3	cervix:	n/a	n/a
7	HA-E2F1	chr19:36426754-36427342	MCF-7	breast:	n/a	n/a
8	SP1	chr19:36426898-36427503	A549	lung:	n/a	chr19:36427405-36427417 chr19:36427406-36427415 chr19:36427407-36427416 chr19:36427406-36427416 chr19:36427406-36427420 chr19:36427405-36427417
9	POLR2A	chr19:36427136-36427336	MCF10A-Er-Src	breast:	n/a	n/a
10	MAX	chr19:36427022-36427332	K562	blood:	n/a	chr19:36427314-36427324
11	YY1	chr19:36426989-36427352	SK-N-SH_RA	brain:	n/a	chr19:36427198-36427209
12	REST	chr19:36426823-36427270	A549	lung:	n/a	chr19:36426848-36426858
13	MAX	chr19:36427099-36427266	HepG2	liver:	n/a	n/a
14	MAX	chr19:36426513-36427735	A549	lung:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
15	REST	chr19:36427086-36427330	PFSK-1	brain:	n/a	n/a
16	ESR1	chr19:36427113-36427324	ECC-1	luminal epithelium:	n/a	n/a
17	YY1	chr19:36426929-36427323	SK-N-SH_RA	brain:	n/a	chr19:36427198-36427209
18	SIN3AK20	chr19:36427119-36427315	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3A	chr19:36426753-36427270	H1-hESC	embryonic stem cell:	n/a	chr19:36426849-36426858
20	SIN3AK20	chr19:36426673-36427273	A549	lung:	n/a	n/a
21	STAT3	chr19:36426862-36427283	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr19:36426974-36427328	HCT-116	colon:	n/a	n/a
23	YY1	chr19:36427102-36427349	HepG2	liver:	n/a	chr19:36427198-36427209
24	TAF1	chr19:36426699-36427464	H1-neurons	neurons:	n/a	n/a
25	HCFC1	chr19:36426693-36427596	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr19:36427139-36427336	MCF10A-Er-Src	breast:	n/a	n/a
27	MAX	chr19:36426896-36427529	HepG2	liver:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
28	YY1	chr19:36426971-36427304	H1-hESC	embryonic stem cell:	n/a	chr19:36427198-36427209
29	TCF12	chr19:36426766-36427953	A549	lung:	n/a	n/a
30	MAX	chr19:36426725-36427494	HCT-116	colon:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
31	ZBTB7A	chr19:36427052-36427820	ECC-1	luminal epithelium:	n/a	chr19:36427222-36427229
32	NRF1	chr19:36426772-36427523	SK-N-SH	brain:	n/a	chr19:36427423-36427432
33	POLR2A	chr19:36427012-36427836	HUVEC	blood vessel:	n/a	n/a
34	GATA2	chr19:36426606-36427248	SH-SY5Y	brain:	n/a	chr19:36426733-36426740
35	POLR2A	chr19:36427001-36427329	PFSK-1	brain:	n/a	n/a
36	E2F4	chr19:36427075-36427415	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr19:36426931-36427352	SK-N-SH	brain:	n/a	n/a
38	REST	chr19:36426518-36428374	H1-neurons	neurons:	n/a	chr19:36426848-36426858 chr19:36427881-36427891
39	MAZ	chr19:36427111-36427630	HepG2	liver:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
40	MAX	chr19:36426728-36427547	A549	lung:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
41	POLR2A	chr19:36426990-36427378	HCT-116	colon:	n/a	n/a
42	MAX	chr19:36426713-36427367	ECC-1	luminal epithelium:	n/a	chr19:36427314-36427324
43	MAX	chr19:36426858-36427516	ECC-1	luminal epithelium:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
44	MXI1	chr19:36426391-36428778	SK-N-SH	brain:	n/a	n/a
45	MAZ	chr19:36426386-36427799	IMR90	lung:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
46	MAX	chr19:36426988-36427518	SK-N-SH	brain:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
47	MAX	chr19:36426662-36427644	MCF-7	breast:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
48	POLR2A	chr19:36427087-36427657	A549	lung:	n/a	n/a
49	POLR2A	chr19:36427122-36427369	Hela-S3	cervix:	n/a	n/a
50	RCOR1	chr19:36426868-36427300	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36231818..36233362-chr19:36425701..36428426,2	MCF-7	breast:
2	chr19:36239375..36241509-chr19:36425781..36428099,2	MCF-7	breast:
3	chr19:36370775..36373541-chr19:36425672..36427378,2	MCF-7	breast:
4	chr19:36390062..36392033-chr19:36425677..36427196,2	MCF-7	breast:
5	chr19:36426653..36429173-chr19:36484778..36487537,2	MCF-7	breast:

Variant related genes	Relation type
LRFN3	TF binding region
ENSG00000267796	Chromatin interaction
ENSG00000243968	Chromatin interaction
ENSG00000126246	Chromatin interaction
ENSG00000205138	Chromatin interaction
ENSG00000167604	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10221461	0.85[ASN][1000 genomes]
rs10221486	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057265	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11878444	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878880	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11879537	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11880835	0.93[ASN][1000 genomes]
rs11880859	0.93[ASN][1000 genomes]
rs11881157	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11882386	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883234	0.91[ASN][1000 genomes]
rs13382036	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242590	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293756	0.93[ASN][1000 genomes]
rs230260	0.81[EUR][1000 genomes]
rs34933126	0.90[EUR][1000 genomes]
rs55686886	0.93[ASN][1000 genomes]
rs56042927	0.93[ASN][1000 genomes]
rs56132631	0.83[ASN][1000 genomes]
rs56132838	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56187901	0.93[ASN][1000 genomes]
rs56230692	0.93[ASN][1000 genomes]
rs56744930	0.90[EUR][1000 genomes]
rs56922307	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57068163	0.90[EUR][1000 genomes]
rs57094555	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57516855	0.85[EUR][1000 genomes]
rs57785375	0.93[ASN][1000 genomes]
rs57962062	0.86[EUR][1000 genomes]
rs58161969	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58291714	0.81[EUR][1000 genomes]
rs58456578	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58504183	0.95[EUR][1000 genomes]
rs58551711	0.95[EUR][1000 genomes]
rs58768499	0.90[ASN][1000 genomes]
rs58976020	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59150589	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59151712	0.93[ASN][1000 genomes]
rs59399698	0.85[EUR][1000 genomes]
rs59416903	0.86[EUR][1000 genomes]
rs59478831	0.81[EUR][1000 genomes]
rs59534183	0.85[EUR][1000 genomes]
rs60073802	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60268250	0.81[EUR][1000 genomes]
rs60276253	0.93[ASN][1000 genomes]
rs60500471	0.93[ASN][1000 genomes]
rs60576074	0.81[EUR][1000 genomes]
rs60869994	0.81[EUR][1000 genomes]
rs60892678	0.93[ASN][1000 genomes]
rs60935148	0.95[EUR][1000 genomes]
rs61510077	0.88[ASN][1000 genomes]
rs61660311	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61672461	0.90[EUR][1000 genomes]
rs7245383	0.93[ASN][1000 genomes]
rs7246259	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246541	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7247000	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247246	0.85[ASN][1000 genomes]
rs7247769	0.93[ASN][1000 genomes]
rs7248253	0.93[ASN][1000 genomes]
rs7248265	0.93[ASN][1000 genomes]
rs7249502	0.93[ASN][1000 genomes]
rs7251380	0.93[ASN][1000 genomes]
rs7251422	0.85[ASN][1000 genomes]
rs7252053	0.85[ASN][1000 genomes]
rs7252526	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252572	0.90[ASN][1000 genomes]
rs7252693	0.93[ASN][1000 genomes]
rs7252839	0.93[ASN][1000 genomes]
rs7253086	0.95[EUR][1000 genomes]
rs7254298	0.93[ASN][1000 genomes]
rs7254335	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7254905	0.93[ASN][1000 genomes]
rs7254994	0.93[ASN][1000 genomes]
rs7255824	0.93[ASN][1000 genomes]
rs7256280	0.90[EUR][1000 genomes]
rs7256433	0.95[EUR][1000 genomes]
rs7256952	0.93[ASN][1000 genomes]
rs7257789	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257911	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258914	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259892	0.93[ASN][1000 genomes]
rs7260613	0.81[EUR][1000 genomes]
rs73590883	0.81[EUR][1000 genomes]
rs73599539	0.90[EUR][1000 genomes]
rs73599540	0.90[EUR][1000 genomes]
rs73599546	0.90[EUR][1000 genomes]
rs73599554	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73599561	0.90[EUR][1000 genomes]
rs73599565	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73599577	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73599586	0.90[EUR][1000 genomes]
rs73599600	0.95[EUR][1000 genomes]
rs73928364	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73928368	0.93[ASN][1000 genomes]
rs73928369	0.93[ASN][1000 genomes]
rs8110868	0.90[EUR][1000 genomes]
rs909135	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909136	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749492	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36426000-36427200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr19:36426400-36427200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:36426400-36427200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:36426400-36427200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:36426400-36427200	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr19:36426400-36427200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr19:36426400-36427200	Flanking Active TSS	Dnd41	blood
8	chr19:36426400-36427200	Flanking Active TSS	Osteobl	bone
9	chr19:36426400-36429400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:36426600-36427200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:36426600-36427200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:36426600-36427200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr19:36426600-36427200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:36426600-36427200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:36426600-36427200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr19:36426600-36427200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr19:36426600-36427200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr19:36426600-36427200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr19:36426600-36427200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:36426600-36427200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr19:36426600-36427200	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr19:36426600-36427200	Flanking Active TSS	Colonic Mucosa	Colon
23	chr19:36426600-36427200	Flanking Active TSS	Fetal Brain Male	brain
24	chr19:36426600-36427200	Flanking Active TSS	Fetal Lung	lung
25	chr19:36426600-36427200	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr19:36426600-36427200	Flanking Active TSS	Placenta	Placenta
27	chr19:36426600-36427200	Flanking Active TSS	Fetal Stomach	stomach
28	chr19:36426600-36427200	Flanking Active TSS	Thymus	Thymus
29	chr19:36426600-36427200	Flanking Active TSS	Hela-S3	cervix
30	chr19:36426600-36427200	Flanking Active TSS	HMEC	breast
31	chr19:36426600-36427200	Flanking Active TSS	HSMM	muscle
32	chr19:36426600-36427200	Flanking Active TSS	HUVEC	blood vessel
33	chr19:36426600-36427200	Flanking Active TSS	NH-A	brain
34	chr19:36426600-36428200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:36426600-36429400	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr19:36426800-36427200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:36426800-36427200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr19:36426800-36427200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:36426800-36427200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
40	chr19:36426800-36427200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr19:36426800-36427200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
42	chr19:36426800-36427200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:36426800-36427200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr19:36426800-36427200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:36426800-36427200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr19:36426800-36427200	Flanking Active TSS	Liver	Liver
47	chr19:36426800-36427200	Flanking Bivalent TSS/Enh	Fetal Heart	heart
48	chr19:36426800-36427200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
49	chr19:36426800-36427600	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr19:36426800-36427800	Active TSS	Fetal Intestine Large	intestine

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