Variant report

Variant	rs862454
Chromosome Location	chr19:39338125-39338126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

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	NFATC1	chr19:39338029-39338727	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:39337621-39338758	K562	blood:	n/a	n/a
6	POLR2A	chr19:39337394-39343937	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr19:39337652-39338705	GM12878	blood:	n/a	n/a
8	HEY1	chr19:39337851-39338430	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:39337647-39338322	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr19:39337391-39338692	A549	lung:	n/a	n/a
12	POLR2A	chr19:39338094-39338281	ProgFib	skin:	n/a	n/a
13	POLR2A	chr19:39337775-39338640	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
15	HEY1	chr19:39337887-39338786	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr19:39337512-39341050	A549	lung:	n/a	n/a
18	POLR2A	chr19:39337355-39338877	GM12892	blood:	n/a	n/a
19	POLR2A	chr19:39337838-39338810	K562	blood:	n/a	n/a
20	POLR2A	chr19:39337631-39338790	K562	blood:	n/a	n/a
21	MTA3	chr19:39337882-39340193	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:39337752-39338802	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:39337886-39338596	GM18505	blood:	n/a	n/a
24	POLR2A	chr19:39337572-39338684	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr19:39337532-39338772	HepG2	liver:	n/a	n/a
26	POLR2A	chr19:39337552-39338626	HCT-116	colon:	n/a	n/a
27	POLR2A	chr19:39337741-39338708	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:39337406-39343729	GM12892	blood:	n/a	n/a
29	GABPA	chr19:39337706-39338390	A549	lung:	n/a	n/a
30	TCF12	chr19:39337395-39344253	A549	lung:	n/a	chr19:39337932-39337939
31	POLR2A	chr19:39337515-39338873	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr19:39337633-39338759	HepG2	liver:	n/a	n/a
33	SIN3AK20	chr19:39337833-39338692	A549	lung:	n/a	n/a
34	POLR2A	chr19:39337525-39340902	GM12892	blood:	n/a	n/a
35	POLR2A	chr19:39337639-39341984	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:39337590-39340763	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr19:39337611-39338722	K562	blood:	n/a	n/a
38	POLR2A	chr19:39337952-39338642	HepG2	liver:	n/a	n/a
39	HEY1	chr19:39337652-39338809	K562	blood:	n/a	n/a
40	POLR2A	chr19:39337567-39338710	MCF-7	breast:	n/a	n/a
41	POLR2A	chr19:39337759-39338666	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:39338013-39338319	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr19:39337910-39338698	U87	brain:	n/a	n/a
44	POLR2A	chr19:39337558-39343695	HL-60	blood:	n/a	n/a
45	POLR2A	chr19:39337516-39338834	U87	brain:	n/a	n/a
46	POLR2A	chr19:39337577-39338716	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:39338094-39338666	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr19:39337675-39343938	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr19:39337642-39338795	GM12892	blood:	n/a	n/a
50	SIX5	chr19:39337474-39344181	A549	lung:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39217331..39220252-chr19:39336372..39338597,2	K562	blood:
2	chr19:39218752..39222924-chr19:39336082..39338597,4	K562	blood:
3	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
4	chr19:39337019..39338579-chr19:39410355..39412359,2	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	chr19:39137328..39141053-chr19:39337803..39340723,6	MCF-7	breast:
8	chr19:39306785..39309520-chr19:39336164..39339038,3	K562	blood:
9	chr19:39310279..39311821-chr19:39336796..39339611,2	K562	blood:
10	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
11	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
12	chr19:39306612..39310061-chr19:39334754..39339038,4	K562	blood:
13	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
14	chr19:39337933..39340213-chr19:39370385..39371920,2	K562	blood:

No data

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

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10403012	0.92[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10411480	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10411844	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10424892	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10425464	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426289	0.85[CHB][hapmap]
rs1078734	0.85[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes]
rs11668179	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11668766	0.97[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11671711	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12974488	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12977821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529713	0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs2075587	0.81[AMR][1000 genomes]
rs2075588	0.82[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs2116852	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2278010	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35829996	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4328569	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802928	0.82[EUR][1000 genomes]
rs7248208	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8108906	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs8110679	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862457	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[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862460	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862461	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862462	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862463	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9789283	0.82[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs862454	ECH1	Cis_1M	lymphoblastoid	RTeQTL
rs862454	ECH1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39325400-39338200	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr19:39325400-39338200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:39326000-39338200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:39326000-39338200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr19:39326000-39338200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr19:39326000-39338200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr19:39326000-39338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:39326000-39338400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:39326000-39338400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:39326000-39338600	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr19:39326200-39338200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr19:39326200-39338400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr19:39326200-39338400	Strong transcription	Fetal Kidney	kidney
14	chr19:39326200-39338800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:39326400-39338200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:39326400-39338400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:39326600-39338200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:39327000-39338400	Strong transcription	NHDF-Ad	bronchial
19	chr19:39327600-39338400	Strong transcription	Osteobl	bone
20	chr19:39327800-39338800	Genic enhancers	Liver	Liver
21	chr19:39328000-39338400	Strong transcription	Aorta	Aorta
22	chr19:39331200-39338600	Genic enhancers	Spleen	Spleen
23	chr19:39331200-39339200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:39331400-39339200	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr19:39331600-39338200	Strong transcription	Fetal Brain Male	brain
26	chr19:39331600-39339000	Genic enhancers	Fetal Thymus	thymus
27	chr19:39331800-39339200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:39332400-39338200	Strong transcription	Small Intestine	intestine
29	chr19:39333200-39338400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr19:39333200-39338800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr19:39333200-39339000	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr19:39333200-39339000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr19:39333400-39338400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:39333600-39339000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:39333800-39338200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:39333800-39338600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr19:39334400-39338400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:39334600-39338200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr19:39335400-39339000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr19:39335600-39338200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:39335600-39339000	Genic enhancers	Fetal Muscle Leg	muscle
42	chr19:39336200-39338200	Genic enhancers	Duodenum Mucosa	Duodenum
43	chr19:39336200-39338600	Genic enhancers	Colon Smooth Muscle	Colon
44	chr19:39336200-39338800	Genic enhancers	Brain Hippocampus Middle	brain
45	chr19:39336200-39338800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:39336200-39338800	Genic enhancers	Pancreas	Pancrea
47	chr19:39336200-39339000	Genic enhancers	Brain Angular Gyrus	brain
48	chr19:39336400-39338200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:39336400-39338800	Genic enhancers	Adipose Nuclei	Adipose
50	chr19:39336400-39339000	Genic enhancers	Fetal Muscle Trunk	muscle

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