Variant report

Variant	rs563622121
Chromosome Location	chr19:39339864-39339865
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	SIN3A	chr19:39339703-39340080	GM12878	blood:	n/a	n/a
2	E2F6	chr19:39339661-39340507	H1-hESC	embryonic stem cell:	n/a	chr19:39340078-39340087 chr19:39340240-39340249 chr19:39339990-39339999 chr19:39340150-39340159 chr19:39339975-39339987 chr19:39340156-39340165 chr19:39340075-39340085
3	ATF3	chr19:39339748-39340324	K562	blood:	n/a	chr19:39340062-39340082
4	RELA	chr19:39339311-39340302	GM19193	blood:	n/a	chr19:39339897-39339906 chr19:39339897-39339906
5	TCF12	chr19:39339823-39340166	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:39339000-39340826	GM12878	blood:	n/a	n/a
7	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
8	SIN3AK20	chr19:39338986-39340426	PANC-1	pancreas:	n/a	n/a
9	FOXM1	chr19:39339585-39341820	GM12878	blood:	n/a	n/a
10	ZBTB33	chr19:39339675-39340316	A549	lung:	n/a	chr19:39339976-39339986
11	NR2F2	chr19:39339695-39340103	K562	blood:	n/a	n/a
12	POLR2A	chr19:39337416-39343742	PFSK-1	brain:	n/a	n/a
13	MYC	chr19:39339759-39340375	K562	blood:	n/a	n/a
14	PML	chr19:39339539-39340826	K562	blood:	n/a	n/a
15	STAT5A	chr19:39339078-39340340	GM12878	blood:	n/a	n/a
16	ELF1	chr19:39339816-39341533	K562	blood:	n/a	chr19:39341273-39341285
17	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
18	POLR2A	chr19:39339056-39341577	MCF10A-Er-Src	breast:	n/a	n/a
19	SIN3AK20	chr19:39337738-39343865	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
21	EP300	chr19:39339700-39340436	GM12878	blood:	n/a	chr19:39340069-39340085
22	TCF12	chr19:39339456-39342246	A549	lung:	n/a	n/a
23	MAX	chr19:39339700-39340975	SK-N-SH	brain:	n/a	chr19:39340626-39340636
24	USF1	chr19:39339846-39340088	HepG2	liver:	n/a	n/a
25	MAX	chr19:39339647-39340218	H1-hESC	embryonic stem cell:	n/a	n/a
26	MYC	chr19:39339749-39341628	MCF10A-Er-Src	breast:	n/a	chr19:39340626-39340636
27	ETS1	chr19:39339459-39340250	A549	lung:	n/a	chr19:39340108-39340119 chr19:39339667-39339678 chr19:39339666-39339680 chr19:39340112-39340119 chr19:39339665-39339678 chr19:39340198-39340211 chr19:39340053-39340064 chr19:39340204-39340215 chr19:39340106-39340120
28	EP300	chr19:39339775-39341094	SK-N-SH	brain:	n/a	chr19:39340665-39340674 chr19:39340069-39340085
29	EGR1	chr19:39339676-39340294	ECC-1	luminal epithelium:	n/a	chr19:39340078-39340087 chr19:39340150-39340159 chr19:39340240-39340249 chr19:39339925-39339938 chr19:39339990-39339999 chr19:39339962-39339969 chr19:39340052-39340062 chr19:39340149-39340158 chr19:39340205-39340218 chr19:39340156-39340165
30	SIN3AK20	chr19:39339492-39341922	MCF-7	breast:	n/a	n/a
31	POLR2A	chr19:39339048-39343662	A549	lung:	n/a	n/a
32	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
33	NRF1	chr19:39339767-39340413	K562	blood:	n/a	chr19:39339991-39340000 chr19:39340077-39340091 chr19:39340149-39340163 chr19:39340236-39340250 chr19:39339986-39340000 chr19:39340077-39340088 chr19:39340074-39340088 chr19:39340146-39340160 chr19:39340239-39340253 chr19:39340241-39340250 chr19:39340155-39340166 chr19:39340149-39340158 chr19:39339989-39340000 chr19:39340079-39340088 chr19:39340239-39340250 chr19:39340045-39340056 chr19:39339989-39340003 chr19:39340077-39340088 chr19:39340155-39340164 chr19:39340149-39340160
34	SPI1	chr19:39339574-39340312	HL-60	blood:	n/a	chr19:39340113-39340120
35	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
36	YY1	chr19:39339585-39341005	GM12878	blood:	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
37	POLR2A	chr19:39339184-39342759	PBDE	blood:	n/a	n/a
38	POLR2A	chr19:39337394-39343937	SK-N-MC	brain:	n/a	n/a
39	NFATC1	chr19:39339045-39340276	GM12878	blood:	n/a	n/a
40	TCF7L2	chr19:39339629-39340237	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr19:39339614-39340857	A549	lung:	n/a	n/a
42	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
43	YY1	chr19:39339718-39340203	A549	lung:	n/a	chr19:39339921-39339930 chr19:39340045-39340059 chr19:39340080-39340094 chr19:39340068-39340082 chr19:39340071-39340085
44	STAT3	chr19:39339807-39340119	MCF10A-Er-Src	breast:	n/a	n/a
45	MYC	chr19:39339864-39339874	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:39338914-39341618	Hela-S3	cervix:	n/a	n/a
47	ETS1	chr19:39339735-39340304	K562	blood:	n/a	chr19:39340108-39340119 chr19:39340112-39340119 chr19:39340198-39340211 chr19:39340053-39340064 chr19:39340204-39340215 chr19:39340106-39340120
48	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
49	CCNT2	chr19:39339527-39340885	K562	blood:	n/a	chr19:39340204-39340213
50	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39226378..39228332-chr19:39339696..39342519,3	K562	blood:
2	chr19:39338960..39343184-chr19:39419440..39422855,6	MCF-7	breast:
3	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
4	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
5	chr19:39339752..39342035-chr9:4984469..4986938,2	MCF-7	breast:
6	chr19:39339763..39342872-chr19:39383611..39385304,3	K562	blood:
7	chr19:39339501..39341434-chr19:39881486..39883567,2	K562	blood:
8	chr19:39304217..39307847-chr19:39338556..39341715,3	MCF-7	breast:
9	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
10	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
11	chr17:4848567..4851401-chr19:39337550..39340336,2	MCF-7	breast:
12	chr19:39338392..39342144-chr19:39367920..39369868,4	K562	blood:
13	chr19:39338470..39342492-chr19:39367140..39370147,4	K562	blood:
14	chr11:67069791..67071479-chr19:39339670..39341309,2	MCF-7	breast:
15	chr19:39137328..39141053-chr19:39337803..39340723,6	MCF-7	breast:
16	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
17	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:
18	chr19:39224740..39226667-chr19:39338777..39342180,3	K562	blood:
19	chr19:39339112..39343595-chr19:39368855..39373078,6	MCF-7	breast:
20	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
21	chr19:39339391..39340580-chr19:39420505..39421476,3	MCF-7	breast:
22	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
23	chr19:39338733..39343337-chr19:39388774..39392675,12	K562	blood:
24	chr19:39339114..39344809-chr19:39363672..39368217,5	MCF-7	breast:
25	chr19:39339689..39340629-chr2:88315565..88316238,2	Hela-S3	cervix:
26	chr19:39339767..39341589-chr19:39404601..39407841,3	K562	blood:
27	chr19:39339409..39344372-chr19:39356868..39363816,11	MCF-7	breast:
28	chr19:39328103..39328842-chr19:39339617..39340595,2	MCF-7	breast:
29	chr19:39108057..39110372-chr19:39339414..39342268,3	K562	blood:
30	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
31	chr19:39337933..39340213-chr19:39370385..39371920,2	K562	blood:

Variant related genes	Relation type
ENSG00000269688	TF binding region
HNRNPL	TF binding region
ENSG00000104823	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000096968	Chromatin interaction
ENSG00000172830	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000108515	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000108518	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000128626	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv16518	chr19:39339686-39341232	Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region	31 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	chr19:39337800-39340000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr19:39338000-39340600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
3	chr19:39338200-39340000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
4	chr19:39338200-39340000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:39338200-39340000	Transcr. at gene 5' and 3'	K562	blood
6	chr19:39338400-39340000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr19:39338400-39340000	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
8	chr19:39338600-39340000	Flanking Active TSS	HUVEC	blood vessel
9	chr19:39338600-39340600	Active TSS	Gastric	stomach
10	chr19:39338600-39341600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:39338600-39343800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr19:39338800-39341400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:39338800-39341600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:39338800-39343400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:39339000-39340000	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:39339000-39340000	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr19:39339000-39340000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:39339000-39340000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:39339000-39340000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr19:39339000-39340000	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr19:39339000-39340000	Flanking Active TSS	Liver	Liver
22	chr19:39339000-39340000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
23	chr19:39339000-39340000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr19:39339000-39340200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:39339000-39340600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr19:39339000-39340600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr19:39339000-39341400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:39339000-39341800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:39339000-39344000	Active TSS	H9 Cell Line	embryonic stem cell
30	chr19:39339200-39340000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr19:39339200-39340000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr19:39339200-39340600	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr19:39339200-39340600	Active TSS	Aorta	Aorta
34	chr19:39339200-39341400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:39339200-39343400	Active TSS	Esophagus	oesophagus
36	chr19:39339400-39340000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr19:39339400-39340000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr19:39339400-39340000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:39339400-39340000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:39339400-39340000	Active TSS	Right Atrium	heart
41	chr19:39339400-39340600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr19:39339400-39340600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:39339400-39340600	Active TSS	Ovary	ovary
44	chr19:39339400-39340600	Active TSS	Pancreas	Pancrea
45	chr19:39339400-39340600	Active TSS	Psoas Muscle	Psoas
46	chr19:39339400-39340600	Active TSS	Right Ventricle	heart
47	chr19:39339400-39340600	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr19:39339400-39340600	Active TSS	Small Intestine	intestine
49	chr19:39339400-39340800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:39339400-39341400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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