Variant report

Variant	rs58504183
Chromosome Location	chr19:36421917-36421918
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	RAD21	chr19:36421765-36423179	A549	lung:	n/a	chr19:36422700-36422714 chr19:36422919-36422932
2	TCF12	chr19:36421790-36423321	A549	lung:	n/a	n/a
3	POLR2A	chr19:36421898-36421943	GM12878	blood:	n/a	n/a
4	SP1	chr19:36421742-36423014	A549	lung:	n/a	chr19:36422401-36422411 chr19:36422764-36422773 chr19:36422531-36422541 chr19:36422759-36422773 chr19:36422531-36422541 chr19:36422762-36422774 chr19:36422879-36422890 chr19:36422763-36422772 chr19:36422764-36422773
5	CUX1	chr19:36421819-36422182	K562	blood:	n/a	n/a
6	BCL3	chr19:36421773-36422833	A549	lung:	n/a	chr19:36422336-36422349
7	SIX5	chr19:36421760-36423090	A549	lung:	n/a	chr19:36422594-36422603 chr19:36422596-36422605 chr19:36422593-36422607
8	SIN3AK20	chr19:36421709-36422830	A549	lung:	n/a	n/a
9	GABPA	chr19:36421905-36422910	A549	lung:	n/a	chr19:36422443-36422454 chr19:36422667-36422676 chr19:36422445-36422454 chr19:36422440-36422454 chr19:36422443-36422457 chr19:36422665-36422674
10	USF1	chr19:36421874-36422883	A549	lung:	n/a	chr19:36422665-36422681
11	REST	chr19:36421906-36423282	A549	lung:	n/a	chr19:36422425-36422438
12	TAF1	chr19:36421895-36422734	A549	lung:	n/a	n/a
13	CTCF	chr19:36421533-36423512	A549	lung:	n/a	chr19:36422697-36422710
14	JUN	chr19:36421665-36423265	K562	blood:	n/a	n/a
15	POLR2A	chr19:36421836-36422827	HepG2	liver:	n/a	n/a
16	RAD21	chr19:36421713-36423240	SK-N-SH	brain:	n/a	chr19:36422700-36422714 chr19:36422919-36422932
17	HCFC1	chr19:36421873-36423244	Hela-S3	cervix:	n/a	n/a
18	REST	chr19:36421807-36422788	H1-neurons	neurons:	n/a	chr19:36422425-36422438

No.	Distal block	Cell Line	Cell type
1	chr19:36390739..36392472-chr19:36420979..36422529,2	K562	blood:
2	chr19:36230402..36233107-chr19:36420998..36423938,3	K562	blood:
3	chr19:36408561..36410368-chr19:36420820..36422349,2	MCF-7	breast:
4	chr19:36208876..36211502-chr19:36420769..36422543,2	K562	blood:
5	chr19:36388372..36393126-chr19:36420797..36424227,6	MCF-7	breast:
6	chr19:36247011..36249990-chr19:36420044..36422413,2	K562	blood:
7	chr19:36379793..36382037-chr19:36419529..36422363,2	MCF-7	breast:
8	chr19:36421247..36424179-chr19:36438110..36439999,2	MCF-7	breast:
9	chr19:36359016..36360950-chr19:36421023..36422625,2	K562	blood:
10	chr19:36393312..36396233-chr19:36420925..36423547,3	K562	blood:
11	chr19:36389300..36392686-chr19:36419635..36422381,3	MCF-7	breast:
12	chr19:36359450..36361367-chr19:36421125..36423142,2	K562	blood:
13	chr19:36390886..36393045-chr19:36420979..36424222,3	K562	blood:
14	chr14:71786963..71787523-chr19:36421838..36422619,2	NB4	blood:
15	chr19:36420760..36422359-chr19:36480786..36482872,2	K562	blood:
16	chr19:36415212..36417969-chr19:36419526..36423356,3	MCF-7	breast:

Variant related genes	Relation type
LRFN3	TF binding region
ENSG00000105290	Chromatin interaction
ENSG00000167595	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000161270	Chromatin interaction
ENSG00000126246	Chromatin interaction
ENSG00000167604	Chromatin interaction
ENSG00000004776	Chromatin interaction
ENSG00000197555	Chromatin interaction
ENSG00000126264	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10221486	0.91[EUR][1000 genomes]
rs1057265	0.95[EUR][1000 genomes]
rs11084834	0.81[EUR][1000 genomes]
rs11878444	0.95[EUR][1000 genomes]
rs11878880	0.87[EUR][1000 genomes]
rs11879537	0.91[EUR][1000 genomes]
rs11880909	0.81[EUR][1000 genomes]
rs11881157	0.91[EUR][1000 genomes]
rs11881358	0.81[EUR][1000 genomes]
rs11881364	0.81[EUR][1000 genomes]
rs11881451	0.81[EUR][1000 genomes]
rs11882386	0.95[EUR][1000 genomes]
rs13382036	0.91[EUR][1000 genomes]
rs16970735	0.81[EUR][1000 genomes]
rs16970737	0.81[EUR][1000 genomes]
rs16970742	0.81[EUR][1000 genomes]
rs16970744	0.81[EUR][1000 genomes]
rs172985	0.81[EUR][1000 genomes]
rs2227909	0.81[EUR][1000 genomes]
rs2242590	0.95[EUR][1000 genomes]
rs230260	0.85[EUR][1000 genomes]
rs230261	0.81[EUR][1000 genomes]
rs230262	0.81[EUR][1000 genomes]
rs230263	0.81[EUR][1000 genomes]
rs230264	0.81[EUR][1000 genomes]
rs230265	0.81[EUR][1000 genomes]
rs230266	0.81[EUR][1000 genomes]
rs230267	0.81[EUR][1000 genomes]
rs230269	0.81[EUR][1000 genomes]
rs2871778	0.81[EUR][1000 genomes]
rs34006827	0.81[EUR][1000 genomes]
rs34933126	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35423326	0.81[EUR][1000 genomes]
rs376240	0.81[EUR][1000 genomes]
rs393116	0.81[EUR][1000 genomes]
rs404299	0.81[EUR][1000 genomes]
rs443186	0.81[EUR][1000 genomes]
rs55797913	0.81[EUR][1000 genomes]
rs55816190	0.81[EUR][1000 genomes]
rs56132838	0.83[EUR][1000 genomes]
rs56744930	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56922307	0.95[EUR][1000 genomes]
rs57053076	0.81[EUR][1000 genomes]
rs57068163	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57094555	0.95[EUR][1000 genomes]
rs57412339	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57516855	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57668132	0.81[EUR][1000 genomes]
rs57962062	0.91[EUR][1000 genomes]
rs58098901	0.81[EUR][1000 genomes]
rs58109577	0.81[EUR][1000 genomes]
rs58161969	0.95[EUR][1000 genomes]
rs58291714	0.85[EUR][1000 genomes]
rs58456578	0.91[EUR][1000 genomes]
rs58551711	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58622306	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58976020	0.91[EUR][1000 genomes]
rs59123406	0.81[EUR][1000 genomes]
rs59150589	0.91[EUR][1000 genomes]
rs59399698	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59416903	0.91[EUR][1000 genomes]
rs59478831	0.85[EUR][1000 genomes]
rs59534183	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59658571	0.81[EUR][1000 genomes]
rs60073802	0.95[EUR][1000 genomes]
rs60268250	0.85[EUR][1000 genomes]
rs60576074	0.85[EUR][1000 genomes]
rs60869994	0.85[EUR][1000 genomes]
rs60935148	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61623584	0.81[EUR][1000 genomes]
rs61660311	0.95[EUR][1000 genomes]
rs61672461	0.95[EUR][1000 genomes]
rs619833	0.81[EUR][1000 genomes]
rs7246259	0.91[EUR][1000 genomes]
rs7246541	0.91[EUR][1000 genomes]
rs7247000	0.91[EUR][1000 genomes]
rs7251744	0.81[EUR][1000 genomes]
rs7252526	0.91[EUR][1000 genomes]
rs7253086	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254335	0.91[EUR][1000 genomes]
rs7256280	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256433	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257789	0.91[EUR][1000 genomes]
rs7257911	0.91[EUR][1000 genomes]
rs7258909	0.81[EUR][1000 genomes]
rs7258914	0.91[EUR][1000 genomes]
rs7260613	0.85[EUR][1000 genomes]
rs73590883	0.85[EUR][1000 genomes]
rs73590895	0.81[EUR][1000 genomes]
rs73599539	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73599540	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73599546	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73599554	0.91[EUR][1000 genomes]
rs73599561	0.95[EUR][1000 genomes]
rs73599565	0.95[EUR][1000 genomes]
rs73599577	0.95[EUR][1000 genomes]
rs73599586	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73599600	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73599602	0.95[EUR][1000 genomes]
rs73928332	0.81[EUR][1000 genomes]
rs73928333	0.81[EUR][1000 genomes]
rs73928364	0.91[EUR][1000 genomes]
rs807660	0.81[EUR][1000 genomes]
rs8106732	0.81[EUR][1000 genomes]
rs8110868	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110926	0.81[EUR][1000 genomes]
rs8111209	0.81[EUR][1000 genomes]
rs8111348	0.81[EUR][1000 genomes]
rs879407	0.81[EUR][1000 genomes]
rs909135	0.90[EUR][1000 genomes]
rs909136	0.90[EUR][1000 genomes]
rs9749325	0.81[EUR][1000 genomes]
rs9749492	0.85[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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36417200-36422000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:36418400-36422000	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:36418400-36422000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr19:36419000-36422000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr19:36419200-36422000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr19:36419400-36422000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr19:36419400-36422000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:36419600-36422000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:36419600-36422000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:36420000-36422000	Weak transcription	Fetal Kidney	kidney
11	chr19:36420400-36422000	Enhancers	Primary hematopoietic stem cells	blood
12	chr19:36420400-36423000	Enhancers	Fetal Thymus	thymus
13	chr19:36420600-36422000	Enhancers	Dnd41	blood
14	chr19:36420600-36422400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr19:36420800-36423000	Enhancers	Spleen	Spleen
16	chr19:36421000-36422000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr19:36421000-36422000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr19:36421000-36422000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:36421000-36422000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr19:36421200-36422000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr19:36421200-36422000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:36421200-36422000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:36421200-36422000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:36421200-36422000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:36421200-36422000	Enhancers	GM12878-XiMat	blood
26	chr19:36421200-36423200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:36421400-36422000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:36421600-36422000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr19:36421600-36422800	Active TSS	Thymus	Thymus
30	chr19:36421800-36422000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:36421800-36422000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr19:36421800-36422000	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr19:36421800-36422000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:36421800-36422000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr19:36421800-36422000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:36421800-36422000	Enhancers	Brain Germinal Matrix	brain
37	chr19:36421800-36422000	Enhancers	Colon Smooth Muscle	Colon
38	chr19:36421800-36422000	Enhancers	Fetal Brain Female	brain
39	chr19:36421800-36422000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr19:36421800-36422000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr19:36421800-36422000	Enhancers	Rectal Smooth Muscle	rectum
42	chr19:36421800-36422000	Enhancers	Hela-S3	cervix
43	chr19:36421800-36422000	Enhancers	HepG2	liver
44	chr19:36421800-36422000	Enhancers	HSMMtube	muscle
45	chr19:36421800-36422000	Enhancers	HUVEC	blood vessel
46	chr19:36421800-36422000	Active TSS	K562	blood
47	chr19:36421800-36422000	Enhancers	NHDF-Ad	bronchial
48	chr19:36421800-36422000	Enhancers	NHEK	skin
49	chr19:36421800-36422000	Enhancers	Osteobl	bone
50	chr19:36421800-36422200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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