Variant report

Variant	rs862457
Chromosome Location	chr19:39338865-39338866
allele	C/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	chr19:39337416-39343742	PFSK-1	brain:	n/a	n/a
2	SIN3AK20	chr19:39337738-39343865	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:39337394-39343937	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:39338484-39343642	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr19:39337512-39341050	A549	lung:	n/a	n/a
10	CTCF	chr19:39338740-39338890	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:39337355-39338877	GM12892	blood:	n/a	n/a
12	MTA3	chr19:39337882-39340193	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:39337406-39343729	GM12892	blood:	n/a	n/a
14	HEY1	chr19:39338860-39340809	K562	blood:	n/a	n/a
15	TCF12	chr19:39337395-39344253	A549	lung:	n/a	chr19:39337932-39337939
16	POLR2A	chr19:39337515-39338873	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:39337525-39340902	GM12892	blood:	n/a	n/a
18	POLR2A	chr19:39337639-39341984	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:39337590-39340763	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr19:39337558-39343695	HL-60	blood:	n/a	n/a
21	POLR2A	chr19:39337675-39343938	H1-hESC	embryonic stem cell:	n/a	n/a
22	CHD1	chr19:39338427-39343932	IMR90	lung:	n/a	chr19:39340621-39340631 chr19:39342661-39342671
23	SIX5	chr19:39337474-39344181	A549	lung:	n/a	n/a
24	MYC	chr19:39338383-39344059	A549	lung:	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 chr19:39338398-39338407 chr19:39342573-39342583 chr19:39342573-39342586 chr19:39342574-39342585
25	POLR2A	chr19:39331012-39342704	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:39332839-39343744	K562	blood:	n/a	n/a
27	POLR2A	chr19:39337489-39340775	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:39337534-39340989	GM12891	blood:	n/a	n/a
29	POLR2A	chr19:39337724-39343531	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr19:39338858-39338875	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr19:39337557-39340750	GM12891	blood:	n/a	n/a
32	POLR2A	chr19:39337594-39338930	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr19:39338740-39338890	GM12873	blood:	n/a	n/a
34	WRNIP1	chr19:39338033-39339993	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:39338714-39338923	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
2	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
3	chr19:39304217..39307847-chr19:39338556..39341715,3	MCF-7	breast:
4	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
5	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
6	chr17:4848567..4851401-chr19:39337550..39340336,2	MCF-7	breast:
7	chr19:39338392..39342144-chr19:39367920..39369868,4	K562	blood:
8	chr19:39338470..39342492-chr19:39367140..39370147,4	K562	blood:
9	chr19:39137328..39141053-chr19:39337803..39340723,6	MCF-7	breast:
10	chr19:39306785..39309520-chr19:39336164..39339038,3	K562	blood:
11	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:
12	chr19:39224740..39226667-chr19:39338777..39342180,3	K562	blood:
13	chr19:39310279..39311821-chr19:39336796..39339611,2	K562	blood:
14	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
15	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
16	chr19:39306612..39310061-chr19:39334754..39339038,4	K562	blood:
17	chr19:39338733..39343337-chr19:39388774..39392675,12	K562	blood:
18	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
19	chr19:39337933..39340213-chr19:39370385..39371920,2	K562	blood:

Variant related genes	Relation type
HNRNPL	TF binding region
ENSG00000269688	TF binding region
ENSG00000267892	Chromatin interaction
ENSG00000108515	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000268756	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000108518	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000104825	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10403012	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10411480	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10411844	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10424892	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10425464	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426289	0.85[CHB][hapmap]
rs1078734	0.84[CHB][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11668179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11668766	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11671711	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12974488	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12977821	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1529713	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2075587	0.83[AMR][1000 genomes]
rs2075588	0.86[AMR][1000 genomes]
rs2116852	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2278010	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35829996	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4328569	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7248208	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7254484	0.85[YRI][hapmap]
rs8108906	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs8110679	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862460	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862461	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862462	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862463	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9789283	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1792915	chr19:39335274-39341182	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a
4	esv1794032	chr19:39335274-39341182	Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a
5	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
6	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
rs862457	ECH1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39331200-39339200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:39331400-39339200	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr19:39331600-39339000	Genic enhancers	Fetal Thymus	thymus
4	chr19:39331800-39339200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:39333200-39339000	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr19:39333200-39339000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr19:39333600-39339000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:39335400-39339000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:39335600-39339000	Genic enhancers	Fetal Muscle Leg	muscle
10	chr19:39336200-39339000	Genic enhancers	Brain Angular Gyrus	brain
11	chr19:39336400-39339000	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr19:39336800-39339000	Genic enhancers	Fetal Intestine Small	intestine
13	chr19:39336800-39339000	Genic enhancers	Stomach Mucosa	stomach
14	chr19:39337000-39339400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:39337600-39339400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
16	chr19:39337600-39339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:39337800-39339000	Genic enhancers	Fetal Intestine Large	intestine
18	chr19:39337800-39339000	Genic enhancers	Fetal Lung	lung
19	chr19:39337800-39339000	Enhancers	Right Atrium	heart
20	chr19:39337800-39339200	Genic enhancers	Brain Cingulate Gyrus	brain
21	chr19:39337800-39339200	Enhancers	Fetal Heart	heart
22	chr19:39337800-39339200	Genic enhancers	Lung	lung
23	chr19:39337800-39339200	Transcr. at gene 5' and 3'	Hela-S3	cervix
24	chr19:39337800-39339400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
25	chr19:39337800-39339600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
26	chr19:39337800-39339800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
27	chr19:39337800-39339800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
28	chr19:39337800-39339800	Transcr. at gene 5' and 3'	A549	lung
29	chr19:39337800-39339800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
30	chr19:39337800-39340000	Transcr. at gene 5' and 3'	Dnd41	blood
31	chr19:39338000-39339000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:39338000-39339000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:39338000-39339000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:39338000-39339000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:39338000-39339400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:39338000-39339600	Transcr. at gene 5' and 3'	HSMM	muscle
37	chr19:39338000-39339800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39338000-39340600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
39	chr19:39338200-39339000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
40	chr19:39338200-39339000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:39338200-39339200	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:39338200-39339200	Genic enhancers	Monocytes-CD14+_RO01746	blood
43	chr19:39338200-39339400	Transcr. at gene 5' and 3'	Right Ventricle	heart
44	chr19:39338200-39339400	Transcr. at gene 5' and 3'	HMEC	breast
45	chr19:39338200-39339800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
46	chr19:39338200-39339800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
47	chr19:39338200-39339800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:39338200-39339800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
49	chr19:39338200-39340000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
50	chr19:39338200-39340000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin

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