Variant report

Variant	rs862462
Chromosome Location	chr19:39344134-39344135
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	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
4	TCF12	chr19:39337395-39344253	A549	lung:	n/a	chr19:39337932-39337939
5	SP1	chr19:39339038-39344135	A549	lung:	n/a	chr19:39343001-39343013 chr19:39342682-39342691 chr19:39341185-39341194 chr19:39341870-39341879 chr19:39341186-39341199 chr19:39342556-39342565 chr19:39340203-39340217 chr19:39342554-39342566 chr19:39340202-39340214 chr19:39341274-39341286 chr19:39341185-39341195 chr19:39341040-39341049 chr19:39341276-39341285 chr19:39343209-39343221 chr19:39340202-39340214 chr19:39342556-39342565 chr19:39342555-39342564 chr19:39341185-39341194 chr19:39342683-39342692 chr19:39343210-39343219 chr19:39342551-39342564 chr19:39340941-39340952 chr19:39342475-39342484 chr19:39342554-39342566 chr19:39343008-39343017 chr19:39342555-39342565 chr19:39343006-39343018 chr19:39342619-39342631 chr19:39341039-39341051 chr19:39341184-39341196 chr19:39343210-39343220 chr19:39340951-39340972 chr19:39342662-39342671 chr19:39342554-39342565 chr19:39343006-39343018 chr19:39343211-39343220 chr19:39340203-39340213 chr19:39342658-39342672 chr19:39341039-39341051 chr19:39341186-39341195 chr19:39342555-39342565 chr19:39340204-39340213 chr19:39342621-39342630 chr19:39340942-39340956 chr19:39342619-39342631 chr19:39341184-39341196 chr19:39343209-39343221 chr19:39343001-39343013 chr19:39343210-39343224 chr19:39342998-39343012 chr19:39340626-39340647 chr19:39341274-39341286 chr19:39340203-39340212
6	SIX5	chr19:39337474-39344181	A549	lung:	n/a	n/a
7	ATF3	chr19:39342880-39344202	A549	lung:	n/a	chr19:39343211-39343220
8	POLR2A	chr19:39344014-39344162	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39341886..39344706-chr19:39358962..39361932,2	K562	blood:
2	chr19:39341787..39344352-chr19:39369532..39371797,3	MCF-7	breast:
3	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
4	chr19:39341602..39344396-chr19:39810637..39813386,2	K562	blood:
5	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
6	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
7	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
8	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:
9	chr19:39343341..39344893-chr19:39367405..39369685,2	K562	blood:
10	chr19:39340592..39344706-chr19:39357882..39361932,6	K562	blood:
11	chr19:39225241..39228879-chr19:39342547..39344492,3	K562	blood:
12	chr19:39341689..39344249-chr19:40949611..40951303,2	K562	blood:
13	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
14	chr19:39137047..39143767-chr19:39341076..39344906,12	MCF-7	breast:
15	chr19:39339114..39344809-chr19:39363672..39368217,5	MCF-7	breast:
16	chr19:39108184..39110512-chr19:39341783..39344242,3	MCF-7	breast:
17	chr19:39340906..39344724-chr19:39389015..39390874,4	MCF-7	breast:
18	chr19:39339409..39344372-chr19:39356868..39363816,11	MCF-7	breast:

Variant related genes	Relation type
HNRNPL	TF binding region
ENSG00000104814	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000268262	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000187994	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10403012	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10411480	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10411844	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10425464	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1078734	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11668179	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11668766	0.83[ASN][1000 genomes]
rs11671711	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12974488	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12977821	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075587	0.82[AFR][1000 genomes]
rs2075588	0.81[AMR][1000 genomes]
rs2116852	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278010	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35829996	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4328569	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802928	0.85[EUR][1000 genomes]
rs7248208	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8110679	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs862454	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862457	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862458	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862460	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862461	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9419	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9789283	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs862462	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39343400-39344200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:39343600-39348200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:39343600-39359800	Weak transcription	Small Intestine	intestine
4	chr19:39343800-39344200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:39343800-39344200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:39343800-39344200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr19:39343800-39344200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr19:39343800-39344200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:39343800-39344200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:39343800-39344200	Enhancers	Fetal Muscle Trunk	muscle
11	chr19:39343800-39344200	Enhancers	Fetal Muscle Leg	muscle
12	chr19:39343800-39344200	Enhancers	Placenta	Placenta
13	chr19:39343800-39344200	Enhancers	Pancreas	Pancrea
14	chr19:39343800-39344400	Enhancers	Primary B cells from peripheral blood	blood
15	chr19:39343800-39344400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr19:39343800-39345000	Enhancers	Primary B cells from cord blood	blood
17	chr19:39343800-39345000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr19:39343800-39345400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:39343800-39346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:39343800-39347200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:39343800-39347200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:39343800-39347400	Weak transcription	Primary T cells from cord blood	blood
23	chr19:39343800-39347400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:39343800-39347800	Weak transcription	Fetal Thymus	thymus
25	chr19:39343800-39348200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:39343800-39348200	Weak transcription	Esophagus	oesophagus
27	chr19:39343800-39348200	Weak transcription	HSMMtube	muscle
28	chr19:39343800-39352400	Weak transcription	HUVEC	blood vessel
29	chr19:39343800-39353000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr19:39343800-39353200	Weak transcription	Fetal Kidney	kidney
31	chr19:39344000-39344200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr19:39344000-39344200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:39344000-39344200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:39344000-39344200	Enhancers	Colon Smooth Muscle	Colon
35	chr19:39344000-39345400	Enhancers	K562	blood
36	chr19:39344000-39346800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr19:39344000-39347000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:39344000-39347000	Weak transcription	Spleen	Spleen
39	chr19:39344000-39347200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:39344000-39347200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:39344000-39347200	Weak transcription	GM12878-XiMat	blood
42	chr19:39344000-39347400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:39344000-39347400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr19:39344000-39347400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:39344000-39347400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr19:39344000-39347400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr19:39344000-39347400	Weak transcription	A549	lung
48	chr19:39344000-39347400	Weak transcription	HepG2	liver
49	chr19:39344000-39347600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr19:39344000-39347600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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