Variant report

Variant	rs862459
Chromosome Location	chr19:39341555-39341556
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	MXI1	chr19:39340646-39341612	K562	blood:	n/a	n/a
2	TAF1	chr19:39340311-39341992	H1-neurons	neurons:	n/a	n/a
3	BCL3	chr19:39338958-39343958	A549	lung:	n/a	chr19:39343210-39343219 chr19:39341504-39341513 chr19:39340067-39340080 chr19:39342053-39342066 chr19:39340700-39340713 chr19:39343077-39343090 chr19:39343075-39343088 chr19:39343069-39343082 chr19:39340693-39340706 chr19:39340664-39340673 chr19:39342783-39342796 chr19:39339897-39339906
4	FOXM1	chr19:39339585-39341820	GM12878	blood:	n/a	n/a
5	MYC	chr19:39341474-39341765	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:39341130-39341562	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:39337416-39343742	PFSK-1	brain:	n/a	n/a
8	MAX	chr19:39341392-39343742	H1-hESC	embryonic stem cell:	n/a	chr19:39342575-39342584 chr19:39342576-39342583 chr19:39342574-39342585 chr19:39342575-39342584 chr19:39343002-39343012 chr19:39342575-39342585 chr19:39342574-39342584 chr19:39342566-39342582 chr19:39342573-39342586 chr19:39342573-39342583 chr19:39342573-39342586 chr19:39342574-39342585
9	TAF1	chr19:39341129-39341642	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr19:39341159-39341879	GM12891	blood:	n/a	n/a
11	SP1	chr19:39339157-39341862	HCT-116	colon:	n/a	chr19:39341185-39341194 chr19:39341186-39341199 chr19:39340203-39340217 chr19:39340202-39340214 chr19:39341274-39341286 chr19:39341185-39341195 chr19:39341040-39341049 chr19:39341276-39341285 chr19:39340202-39340214 chr19:39341185-39341194 chr19:39340941-39340952 chr19:39341039-39341051 chr19:39341184-39341196 chr19:39340951-39340972 chr19:39340203-39340213 chr19:39341039-39341051 chr19:39341186-39341195 chr19:39340204-39340213 chr19:39340942-39340956 chr19:39341184-39341196 chr19:39340626-39340647 chr19:39341274-39341286 chr19:39340203-39340212
12	HEY1	chr19:39341113-39343619	K562	blood:	n/a	n/a
13	POLR2A	chr19:39339056-39341577	MCF10A-Er-Src	breast:	n/a	n/a
14	SIN3AK20	chr19:39337738-39343865	PANC-1	pancreas:	n/a	n/a
15	GABPA	chr19:39340492-39341696	MCF-7	breast:	n/a	chr19:39341241-39341252 chr19:39341241-39341255 chr19:39341243-39341252
16	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
17	RCOR1	chr19:39341273-39341601	HepG2	liver:	n/a	n/a
18	TCF12	chr19:39339456-39342246	A549	lung:	n/a	n/a
19	CTCF	chr19:39341500-39341650	SAEC	small airway:	n/a	n/a
20	MYC	chr19:39341507-39341608	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:39341101-39341913	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:39341137-39341975	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr19:39341117-39342789	GM12891	blood:	n/a	n/a
24	MYC	chr19:39339749-39341628	MCF10A-Er-Src	breast:	n/a	chr19:39340626-39340636
25	GATA3	chr19:39341164-39341682	T-47D	breast:	n/a	n/a
26	SIN3AK20	chr19:39339492-39341922	MCF-7	breast:	n/a	n/a
27	POLR2A	chr19:39339048-39343662	A549	lung:	n/a	n/a
28	EGR1	chr19:39339636-39341856	HCT-116	colon:	n/a	chr19:39340078-39340087 chr19:39341268-39341275 chr19:39340666-39340679 chr19:39340150-39340159 chr19:39340240-39340249 chr19:39339925-39339938 chr19:39340558-39340572 chr19:39339990-39339999 chr19:39341242-39341251 chr19:39339962-39339969 chr19:39340052-39340062 chr19:39340666-39340676 chr19:39340149-39340158 chr19:39340205-39340218 chr19:39340156-39340165
29	POLR2A	chr19:39340859-39342060	A549	lung:	n/a	n/a
30	GABPA	chr19:39339841-39341588	K562	blood:	n/a	chr19:39339991-39340000 chr19:39340077-39340091 chr19:39340149-39340163 chr19:39340236-39340250 chr19:39339986-39340000 chr19:39340077-39340088 chr19:39341241-39341252 chr19:39340074-39340088 chr19:39340146-39340160 chr19:39340239-39340253 chr19:39340241-39340250 chr19:39340155-39340166 chr19:39341241-39341255 chr19:39340149-39340158 chr19:39339989-39340000 chr19:39340079-39340088 chr19:39340239-39340250 chr19:39339989-39340003 chr19:39340155-39340164 chr19:39341243-39341252 chr19:39340149-39340160
31	POLR2A	chr19:39339184-39342759	PBDE	blood:	n/a	n/a
32	PML	chr19:39341131-39341785	MCF-7	breast:	n/a	n/a
33	POLR2A	chr19:39337394-39343937	SK-N-MC	brain:	n/a	n/a
34	CTCF	chr19:39341440-39341590	GM06990	blood:	n/a	n/a
35	YY1	chr19:39339562-39342203	A549	lung:	n/a	chr19:39339921-39339930 chr19:39339658-39339666 chr19:39340045-39340059 chr19:39340080-39340094 chr19:39340838-39340847 chr19:39340068-39340082 chr19:39340665-39340674 chr19:39340071-39340085
36	TCF12	chr19:39341180-39342859	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr19:39338914-39341618	Hela-S3	cervix:	n/a	n/a
38	YY1	chr19:39339921-39341577	ECC-1	luminal epithelium:	n/a	chr19:39339921-39339930 chr19:39340045-39340059 chr19:39340080-39340094 chr19:39340838-39340847 chr19:39340068-39340082 chr19:39340665-39340674 chr19:39340071-39340085
39	MAX	chr19:39339535-39343669	HCT-116	colon:	n/a	chr19:39342575-39342584 chr19:39342576-39342583 chr19:39342574-39342585 chr19:39342575-39342584 chr19:39343002-39343012 chr19:39342575-39342585 chr19:39342574-39342584 chr19:39342566-39342582 chr19:39342573-39342586 chr19:39340626-39340636 chr19:39342573-39342583 chr19:39342573-39342586 chr19:39342574-39342585
40	CEBPB	chr19:39341163-39341699	K562	blood:	n/a	n/a
41	POLR2A	chr19:39341115-39341654	HUVEC	blood vessel:	n/a	n/a
42	SRF	chr19:39340346-39341621	MCF-7	breast:	n/a	chr19:39341045-39341058 chr19:39340666-39340676 chr19:39341042-39341060
43	SIN3AK20	chr19:39340601-39342098	A549	lung:	n/a	n/a
44	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
45	GATA3	chr19:39341182-39341563	MCF-7	breast:	n/a	n/a
46	MAX	chr19:39341041-39343734	K562	blood:	n/a	chr19:39342575-39342584 chr19:39342576-39342583 chr19:39342574-39342585 chr19:39342575-39342584 chr19:39343002-39343012 chr19:39342575-39342585 chr19:39342574-39342584 chr19:39342566-39342582 chr19:39342573-39342586 chr19:39342573-39342583 chr19:39342573-39342586 chr19:39342574-39342585
47	CTCF	chr19:39341520-39341670	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:39339656-39343592	GM18951	blood:	n/a	n/a
49	E2F6	chr19:39339020-39341823	A549	lung:	n/a	chr19:39340078-39340087 chr19:39341242-39341251 chr19:39340838-39340847 chr19:39341005-39341020 chr19:39341007-39341019 chr19:39340240-39340249 chr19:39339990-39339999 chr19:39340150-39340159 chr19:39339975-39339987 chr19:39340771-39340785 chr19:39340156-39340165 chr19:39340075-39340085
50	MYBL2	chr19:39339493-39341590	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39226378..39228332-chr19:39339696..39342519,3	K562	blood:
2	chr19:39340139..39342549-chr19:39383529..39386442,2	MCF-7	breast:
3	chr19:39338960..39343184-chr19:39419440..39422855,6	MCF-7	breast:
4	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
5	chr19:38893264..38895978-chr19:39340017..39342861,2	MCF-7	breast:
6	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
7	chr19:39339752..39342035-chr9:4984469..4986938,2	MCF-7	breast:
8	chr19:39339763..39342872-chr19:39383611..39385304,3	K562	blood:
9	chr19:39340101..39342858-chr19:39435561..39437371,2	K562	blood:
10	chr19:39304217..39307847-chr19:39338556..39341715,3	MCF-7	breast:
11	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
12	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
13	chr19:39338392..39342144-chr19:39367920..39369868,4	K562	blood:
14	chr19:39108186..39111004-chr19:39340137..39342268,2	K562	blood:
15	chr19:39338470..39342492-chr19:39367140..39370147,4	K562	blood:
16	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
17	chr19:39341057..39343314-chr19:39902630..39904241,2	MCF-7	breast:
18	chr19:39226722..39228357-chr19:39340194..39343791,3	K562	blood:
19	chr19:39339873..39342860-chr19:39409643..39412054,2	MCF-7	breast:
20	chr19:39233778..39236095-chr19:39340274..39342606,2	K562	blood:
21	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:
22	chr19:39224740..39226667-chr19:39338777..39342180,3	K562	blood:
23	chr19:39340592..39344706-chr19:39357882..39361932,6	K562	blood:
24	chr19:39260117..39262134-chr19:39341376..39343069,2	K562	blood:
25	chr19:39340110..39342981-chr19:39406423..39409674,4	MCF-7	breast:
26	chr19:39339112..39343595-chr19:39368855..39373078,6	MCF-7	breast:
27	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
28	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
29	chr19:39341273..39343616-chr19:39405354..39407525,2	MCF-7	breast:
30	chr19:39137047..39143767-chr19:39341076..39344906,12	MCF-7	breast:
31	chr19:39338733..39343337-chr19:39388774..39392675,12	K562	blood:
32	chr19:39339114..39344809-chr19:39363672..39368217,5	MCF-7	breast:
33	chr19:39026179..39027940-chr19:39341068..39343027,2	MCF-7	breast:
34	chr19:39339767..39341589-chr19:39404601..39407841,3	K562	blood:
35	chr19:39340906..39344724-chr19:39389015..39390874,4	MCF-7	breast:
36	chr19:39339409..39344372-chr19:39356868..39363816,11	MCF-7	breast:
37	chr19:39200022..39202960-chr19:39340126..39342618,2	K562	blood:
38	chr19:39108057..39110372-chr19:39339414..39342268,3	K562	blood:
39	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
40	chr19:39340477..39342745-chr7:150775717..150778073,2	MCF-7	breast:
41	chr19:39340089..39343125-chr19:39404601..39408323,3	K562	blood:

Variant related genes	Relation type
HNRNPL	TF binding region
ENSG00000068903	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000268055	Chromatin interaction
ENSG00000269190	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000164896	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000096968	Chromatin interaction
ENSG00000104825	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1103435	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113123	0.95[EUR][1000 genomes]
rs2113124	0.92[EUR][1000 genomes]
rs2278009	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278011	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278012	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2318459	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508822	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67859595	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246134	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255774	0.97[ASN][1000 genomes]
rs8104416	0.92[EUR][1000 genomes]
rs8104420	0.94[EUR][1000 genomes]
rs862455	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862464	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9789283	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3327857	chr19:39339137-39341985	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs862459	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL
rs862459	ECH1	Cis_1M	lymphoblastoid	RTeQTL
rs862459	HNRNPL	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39338600-39341600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:39338600-39343800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:39338800-39341600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:39338800-39343400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:39339000-39341800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:39339000-39344000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:39339200-39343400	Active TSS	Esophagus	oesophagus
8	chr19:39339400-39341600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:39339400-39341600	Active TSS	Placenta Amnion	Placenta Amnion
10	chr19:39339400-39341600	Active TSS	HSMMtube	muscle
11	chr19:39339400-39341800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr19:39339400-39342000	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr19:39339600-39341600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:39339600-39341600	Active TSS	Brain Germinal Matrix	brain
15	chr19:39339600-39341600	Active TSS	Colonic Mucosa	Colon
16	chr19:39339600-39343200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr19:39339800-39341600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:39339800-39341600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:39339800-39341600	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr19:39339800-39341600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:39339800-39341600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:39339800-39341600	Active TSS	Brain Substantia Nigra	brain
23	chr19:39339800-39341600	Active TSS	Fetal Stomach	stomach
24	chr19:39339800-39341800	Active TSS	Brain Hippocampus Middle	brain
25	chr19:39339800-39342000	Active TSS	Thymus	Thymus
26	chr19:39339800-39343400	Active TSS	Brain Angular Gyrus	brain
27	chr19:39339800-39343400	Active TSS	Brain Cingulate Gyrus	brain
28	chr19:39339800-39343400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr19:39339800-39343400	Active TSS	Colon Smooth Muscle	Colon
30	chr19:39339800-39343800	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr19:39339800-39344000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr19:39339800-39344000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:39340000-39341600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:39340000-39341600	Active TSS	Liver	Liver
35	chr19:39340000-39341600	Active TSS	Fetal Intestine Small	intestine
36	chr19:39340000-39341600	Active TSS	HepG2	liver
37	chr19:39340000-39341600	Active TSS	K562	blood
38	chr19:39340000-39343400	Active TSS	Brain Anterior Caudate	brain
39	chr19:39340000-39344000	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr19:39340800-39342400	Active TSS	Right Atrium	heart
41	chr19:39341200-39341600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:39341200-39341600	Active TSS	Fetal Brain Male	brain
43	chr19:39341200-39341600	Active TSS	Fetal Lung	lung
44	chr19:39341200-39342600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:39341200-39342600	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr19:39341200-39343800	Active TSS	Fetal Kidney	kidney
47	chr19:39341400-39341600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:39341400-39341600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:39341400-39341600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr19:39341400-39341600	Active TSS	Primary T killer memory cells from peripheral blood	blood

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