Variant report

Variant	rs10421087
Chromosome Location	chr19:39339263-39339264
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	chr19:39339000-39340826	GM12878	blood:	n/a	n/a
2	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
3	SIN3AK20	chr19:39338986-39340426	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39337416-39343742	PFSK-1	brain:	n/a	n/a
5	STAT5A	chr19:39339078-39340340	GM12878	blood:	n/a	n/a
6	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
7	POLR2A	chr19:39339056-39341577	MCF10A-Er-Src	breast:	n/a	n/a
8	HEY1	chr19:39339119-39339515	K562	blood:	n/a	n/a
9	SIN3AK20	chr19:39337738-39343865	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
11	BCLAF1	chr19:39338905-39339447	GM12878	blood:	n/a	n/a
12	NFATC1	chr19:39339147-39339615	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:39339048-39343662	A549	lung:	n/a	n/a
14	POLR2A	chr19:39339139-39339414	A549	lung:	n/a	n/a
15	POLR2A	chr19:39339184-39342759	PBDE	blood:	n/a	n/a
16	POLR2A	chr19:39337394-39343937	SK-N-MC	brain:	n/a	n/a
17	NFATC1	chr19:39339045-39340276	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:39338914-39341618	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
20	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
21	RELA	chr19:39339183-39340294	GM15510	blood:	n/a	chr19:39339897-39339906 chr19:39339897-39339906
22	POLR2A	chr19:39339029-39341923	K562	blood:	n/a	n/a
23	RFX5	chr19:39339234-39341794	SK-N-SH	brain:	n/a	chr19:39341103-39341112 chr19:39341165-39341174
24	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:39338943-39341084	HUVEC	blood vessel:	n/a	n/a
26	MYC	chr19:39339228-39342813	K562	blood:	n/a	chr19:39342575-39342584 chr19:39342576-39342583 chr19:39342574-39342585 chr19:39342575-39342584 chr19:39342575-39342585 chr19:39342574-39342584 chr19:39342566-39342582 chr19:39342573-39342586 chr19:39340626-39340636 chr19:39342573-39342583 chr19:39342573-39342586 chr19:39342574-39342585
27	POLR2A	chr19:39338484-39343642	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr19:39339226-39342861	K562	blood:	n/a	n/a
29	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr19:39339108-39343569	K562	blood:	n/a	n/a
31	POLR2A	chr19:39339094-39339422	ECC-1	luminal epithelium:	n/a	n/a
32	EP300	chr19:39339016-39340376	A549	lung:	n/a	chr19:39340069-39340085
33	ELF1	chr19:39338969-39340346	A549	lung:	n/a	n/a
34	FOSL2	chr19:39339175-39342790	A549	lung:	n/a	chr19:39340619-39340628 chr19:39342240-39342252 chr19:39341164-39341173 chr19:39340012-39340021
35	POLR2A	chr19:39339155-39340882	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr19:39339214-39339338	MCF-7	breast:	n/a	n/a
37	SP1	chr19:39339150-39343979	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
38	GATA3	chr19:39339013-39344076	A549	lung:	n/a	chr19:39343447-39343456
39	POLR2A	chr19:39337512-39341050	A549	lung:	n/a	n/a
40	POLR2A	chr19:39339201-39340307	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr19:39338974-39340903	HL-60	blood:	n/a	n/a
42	POLR2A	chr19:39338993-39340320	HepG2	liver:	n/a	n/a
43	MTA3	chr19:39337882-39340193	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:39338967-39340804	IMR90	lung:	n/a	n/a
45	CHD1	chr19:39339202-39340044	H1-hESC	embryonic stem cell:	n/a	n/a
46	TEAD4	chr19:39339190-39342184	K562	blood:	n/a	n/a
47	ATF3	chr19:39338999-39341797	A549	lung:	n/a	chr19:39340062-39340082
48	POLR2A	chr19:39337406-39343729	GM12892	blood:	n/a	n/a
49	REST	chr19:39339070-39342802	A549	lung:	n/a	chr19:39342505-39342515 chr19:39342498-39342511 chr19:39341788-39341808 chr19:39342495-39342508 chr19:39341788-39341808 chr19:39342491-39342511 chr19:39341790-39341800 chr19:39342495-39342508
50	HEY1	chr19:39338860-39340809	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39338960..39343184-chr19:39419440..39422855,6	MCF-7	breast:
2	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
3	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
4	chr19:39304217..39307847-chr19:39338556..39341715,3	MCF-7	breast:
5	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
6	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
7	chr17:4848567..4851401-chr19:39337550..39340336,2	MCF-7	breast:
8	chr19:39338392..39342144-chr19:39367920..39369868,4	K562	blood:
9	chr19:39338470..39342492-chr19:39367140..39370147,4	K562	blood:
10	chr19:39137328..39141053-chr19:39337803..39340723,6	MCF-7	breast:
11	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
12	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:
13	chr19:39224740..39226667-chr19:39338777..39342180,3	K562	blood:
14	chr19:39310279..39311821-chr19:39336796..39339611,2	K562	blood:
15	chr19:39339112..39343595-chr19:39368855..39373078,6	MCF-7	breast:
16	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
17	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
18	chr19:39338733..39343337-chr19:39388774..39392675,12	K562	blood:
19	chr19:39339114..39344809-chr19:39363672..39368217,5	MCF-7	breast:
20	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
21	chr19:39337933..39340213-chr19:39370385..39371920,2	K562	blood:

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

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10418861	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10421560	1.00[YRI][hapmap]
rs13344413	1.00[YRI][hapmap]
rs3786839	1.00[YRI][hapmap]
rs7251725	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7251903	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39337000-39339400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39337600-39339400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
3	chr19:39337600-39339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:39337800-39339400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
5	chr19:39337800-39339600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
6	chr19:39337800-39339800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr19:39337800-39339800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
8	chr19:39337800-39339800	Transcr. at gene 5' and 3'	A549	lung
9	chr19:39337800-39339800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
10	chr19:39337800-39340000	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr19:39338000-39339400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:39338000-39339600	Transcr. at gene 5' and 3'	HSMM	muscle
13	chr19:39338000-39339800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:39338000-39340600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
15	chr19:39338200-39339400	Transcr. at gene 5' and 3'	Right Ventricle	heart
16	chr19:39338200-39339400	Transcr. at gene 5' and 3'	HMEC	breast
17	chr19:39338200-39339800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
18	chr19:39338200-39339800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
19	chr19:39338200-39339800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:39338200-39339800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
21	chr19:39338200-39340000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
22	chr19:39338200-39340000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:39338200-39340000	Transcr. at gene 5' and 3'	K562	blood
24	chr19:39338400-39339400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr19:39338400-39339400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:39338400-39339400	Transcr. at gene 5' and 3'	NHLF	lung
27	chr19:39338400-39339600	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr19:39338400-39339800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:39338400-39339800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:39338400-39339800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:39338400-39339800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
32	chr19:39338400-39339800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr19:39338400-39339800	Transcr. at gene 5' and 3'	NHEK	skin
34	chr19:39338400-39339800	Transcr. at gene 5' and 3'	Osteobl	bone
35	chr19:39338400-39340000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr19:39338400-39340000	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
37	chr19:39338600-39339400	Transcr. at gene 5' and 3'	Placenta	Placenta
38	chr19:39338600-39339600	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
39	chr19:39338600-39339600	Active TSS	Fetal Kidney	kidney
40	chr19:39338600-39339800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:39338600-39339800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
42	chr19:39338600-39339800	Flanking Active TSS	Fetal Brain Female	brain
43	chr19:39338600-39339800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
44	chr19:39338600-39340000	Flanking Active TSS	HUVEC	blood vessel
45	chr19:39338600-39340600	Active TSS	Gastric	stomach
46	chr19:39338600-39341600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:39338600-39343800	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr19:39338800-39339400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
49	chr19:39338800-39339400	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:39338800-39339600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell

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