Variant report

Variant	rs60869318
Chromosome Location	chr19:39338711-39338712
allele	A/C
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	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	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
9	HEY1	chr19:39337887-39338786	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:39338484-39343642	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr19:39337512-39341050	A549	lung:	n/a	n/a
13	POLR2A	chr19:39337355-39338877	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:39337838-39338810	K562	blood:	n/a	n/a
15	POLR2A	chr19:39337631-39338790	K562	blood:	n/a	n/a
16	MTA3	chr19:39337882-39340193	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:39337752-39338802	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:39337532-39338772	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:39337406-39343729	GM12892	blood:	n/a	n/a
20	TCF12	chr19:39337395-39344253	A549	lung:	n/a	chr19:39337932-39337939
21	POLR2A	chr19:39337515-39338873	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:39337633-39338759	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:39337525-39340902	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:39337639-39341984	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:39337590-39340763	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:39337611-39338722	K562	blood:	n/a	n/a
27	HEY1	chr19:39337652-39338809	K562	blood:	n/a	n/a
28	POLR2A	chr19:39337558-39343695	HL-60	blood:	n/a	n/a
29	POLR2A	chr19:39337516-39338834	U87	brain:	n/a	n/a
30	POLR2A	chr19:39337577-39338716	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:39338370-39338742	HCT-116	colon:	n/a	n/a
32	POLR2A	chr19:39337675-39343938	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr19:39337642-39338795	GM12892	blood:	n/a	n/a
34	CHD1	chr19:39338427-39343932	IMR90	lung:	n/a	chr19:39340621-39340631 chr19:39342661-39342671
35	SIX5	chr19:39337474-39344181	A549	lung:	n/a	n/a
36	POLR2A	chr19:39337636-39338843	H1-hESC	embryonic stem cell:	n/a	n/a
37	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
38	POLR2A	chr19:39337690-39338856	GM12891	blood:	n/a	n/a
39	POLR2A	chr19:39337816-39338735	HL-60	blood:	n/a	n/a
40	POLR2A	chr19:39331012-39342704	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:39337385-39338773	K562	blood:	n/a	n/a
42	POLR2A	chr19:39332839-39343744	K562	blood:	n/a	n/a
43	POLR2A	chr19:39337489-39340775	GM12891	blood:	n/a	n/a
44	POLR2A	chr19:39337534-39340989	GM12891	blood:	n/a	n/a
45	POLR2A	chr19:39337724-39343531	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr19:39337557-39340750	GM12891	blood:	n/a	n/a
47	POLR2A	chr19:39337594-39338930	H1-hESC	embryonic stem cell:	n/a	n/a
48	JUND	chr19:39337768-39338794	A549	lung:	n/a	chr19:39338223-39338232
49	WRNIP1	chr19:39338033-39339993	GM12878	blood:	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	chr19:39310279..39311821-chr19:39336796..39339611,2	K562	blood:
13	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
14	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
15	chr19:39306612..39310061-chr19:39334754..39339038,4	K562	blood:
16	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
17	chr19:39337933..39340213-chr19:39370385..39371920,2	K562	blood:

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

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs73539687	1.00[AMR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39326200-39338800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr19:39327800-39338800	Genic enhancers	Liver	Liver
3	chr19:39331200-39339200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:39331400-39339200	Genic enhancers	Primary B cells from peripheral blood	blood
5	chr19:39331600-39339000	Genic enhancers	Fetal Thymus	thymus
6	chr19:39331800-39339200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:39333200-39338800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr19:39333200-39339000	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr19:39333200-39339000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:39333600-39339000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:39335400-39339000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:39335600-39339000	Genic enhancers	Fetal Muscle Leg	muscle
13	chr19:39336200-39338800	Genic enhancers	Brain Hippocampus Middle	brain
14	chr19:39336200-39338800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:39336200-39338800	Genic enhancers	Pancreas	Pancrea
16	chr19:39336200-39339000	Genic enhancers	Brain Angular Gyrus	brain
17	chr19:39336400-39338800	Genic enhancers	Adipose Nuclei	Adipose
18	chr19:39336400-39339000	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr19:39336600-39338800	Genic enhancers	Primary T cells from cord blood	blood
20	chr19:39336800-39339000	Genic enhancers	Fetal Intestine Small	intestine
21	chr19:39336800-39339000	Genic enhancers	Stomach Mucosa	stomach
22	chr19:39337000-39339400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:39337600-39338800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:39337600-39338800	Genic enhancers	Primary B cells from cord blood	blood
25	chr19:39337600-39338800	Genic enhancers	Thymus	Thymus
26	chr19:39337600-39339400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
27	chr19:39337600-39339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:39337800-39338800	Genic enhancers	Esophagus	oesophagus
29	chr19:39337800-39339000	Genic enhancers	Fetal Intestine Large	intestine
30	chr19:39337800-39339000	Genic enhancers	Fetal Lung	lung
31	chr19:39337800-39339000	Enhancers	Right Atrium	heart
32	chr19:39337800-39339200	Genic enhancers	Brain Cingulate Gyrus	brain
33	chr19:39337800-39339200	Enhancers	Fetal Heart	heart
34	chr19:39337800-39339200	Genic enhancers	Lung	lung
35	chr19:39337800-39339200	Transcr. at gene 5' and 3'	Hela-S3	cervix
36	chr19:39337800-39339400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
37	chr19:39337800-39339600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
38	chr19:39337800-39339800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
39	chr19:39337800-39339800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
40	chr19:39337800-39339800	Transcr. at gene 5' and 3'	A549	lung
41	chr19:39337800-39339800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
42	chr19:39337800-39340000	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr19:39338000-39338800	Genic enhancers	Colonic Mucosa	Colon
44	chr19:39338000-39338800	Genic enhancers	Fetal Stomach	stomach
45	chr19:39338000-39338800	Genic enhancers	Rectal Mucosa Donor 29	rectum
46	chr19:39338000-39339000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:39338000-39339000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:39338000-39339000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:39338000-39339000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:39338000-39339400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin

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