Variant report

Variant	rs571567279
Chromosome Location	chr19:39341146-39341147
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	STAT3	chr19:39341060-39341519	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr19:39340646-39341612	K562	blood:	n/a	n/a
3	TAF1	chr19:39340311-39341992	H1-neurons	neurons:	n/a	n/a
4	STAT3	chr19:39340681-39341474	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr19:39340881-39341504	MCF10A-Er-Src	breast:	n/a	n/a
6	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
7	FOXM1	chr19:39339585-39341820	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:39341130-39341562	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr19:39337416-39343742	PFSK-1	brain:	n/a	n/a
10	TAF1	chr19:39341129-39341642	SK-N-SH	brain:	n/a	n/a
11	ELF1	chr19:39339816-39341533	K562	blood:	n/a	chr19:39341273-39341285
12	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
13	FOS	chr19:39340586-39341488	MCF10A-Er-Src	breast:	n/a	chr19:39340619-39340628 chr19:39341164-39341173
14	HEY1	chr19:39341113-39343619	K562	blood:	n/a	n/a
15	USF1	chr19:39340761-39341224	SK-N-SH_RA	brain:	n/a	n/a
16	POLR2A	chr19:39339056-39341577	MCF10A-Er-Src	breast:	n/a	n/a
17	SIN3AK20	chr19:39337738-39343865	PANC-1	pancreas:	n/a	n/a
18	CCNT2	chr19:39341134-39341516	K562	blood:	n/a	n/a
19	GABPA	chr19:39340492-39341696	MCF-7	breast:	n/a	chr19:39341241-39341252 chr19:39341241-39341255 chr19:39341243-39341252
20	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
21	IRF1	chr19:39340515-39341547	K562	blood:	n/a	chr19:39341037-39341051 chr19:39341503-39341513 chr19:39341501-39341521 chr19:39341274-39341288 chr19:39341503-39341517 chr19:39341497-39341514
22	TCF12	chr19:39339456-39342246	A549	lung:	n/a	n/a
23	FOS	chr19:39340473-39341347	GM12878	blood:	n/a	chr19:39340619-39340628 chr19:39341164-39341173
24	POLR2A	chr19:39341101-39341913	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:39341137-39341975	H1-hESC	embryonic stem cell:	n/a	n/a
26	STAT3	chr19:39340874-39341453	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr19:39341117-39342789	GM12891	blood:	n/a	n/a
28	MYC	chr19:39339749-39341628	MCF10A-Er-Src	breast:	n/a	chr19:39340626-39340636
29	SIN3AK20	chr19:39339492-39341922	MCF-7	breast:	n/a	n/a
30	POLR2A	chr19:39339048-39343662	A549	lung:	n/a	n/a
31	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
32	POLR2A	chr19:39340859-39342060	A549	lung:	n/a	n/a
33	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
34	POLR2A	chr19:39339184-39342759	PBDE	blood:	n/a	n/a
35	PML	chr19:39341131-39341785	MCF-7	breast:	n/a	n/a
36	SMC3	chr19:39340610-39341494	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr19:39337394-39343937	SK-N-MC	brain:	n/a	n/a
38	SIN3AK20	chr19:39341116-39341528	SK-N-SH	brain:	n/a	n/a
39	PBX3	chr19:39340456-39341475	GM12878	blood:	n/a	chr19:39341331-39341340
40	FOS	chr19:39340521-39341307	Hela-S3	cervix:	n/a	chr19:39340619-39340628 chr19:39341164-39341173
41	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
42	ZKSCAN1	chr19:39340539-39341334	Hela-S3	cervix:	n/a	chr19:39341317-39341330
43	STAT3	chr19:39340874-39341455	MCF10A-Er-Src	breast:	n/a	n/a
44	BHLHE40	chr19:39339906-39341147	HepG2	liver:	n/a	chr19:39340136-39340152 chr19:39340699-39340715
45	JUND	chr19:39340711-39341370	HepG2	liver:	n/a	chr19:39341164-39341173
46	E2F4	chr19:39340503-39341211	GM12878	blood:	n/a	chr19:39340838-39340847 chr19:39341005-39341020 chr19:39341007-39341019 chr19:39340771-39340785
47	POLR2A	chr19:39338914-39341618	Hela-S3	cervix:	n/a	n/a
48	YY1	chr19:39339921-39341577	ECC-1	luminal epithelium:	n/a	chr19:39339921-39339930 chr19:39340045-39340059 chr19:39340080-39340094 chr19:39340838-39340847 chr19:39340068-39340082 chr19:39340665-39340674 chr19:39340071-39340085
49	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
50	POLR2A	chr19:39341115-39341654	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39226378..39228332-chr19:39339696..39342519,3	K562	blood:
2	chr19:39340139..39342549-chr19:39383529..39386442,2	MCF-7	breast:
3	chr19:39338960..39343184-chr19:39419440..39422855,6	MCF-7	breast:
4	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
5	chr19:38893264..38895978-chr19:39340017..39342861,2	MCF-7	breast:
6	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
7	chr19:39339752..39342035-chr9:4984469..4986938,2	MCF-7	breast:
8	chr19:39339763..39342872-chr19:39383611..39385304,3	K562	blood:
9	chr19:39339501..39341434-chr19:39881486..39883567,2	K562	blood:
10	chr19:39340101..39342858-chr19:39435561..39437371,2	K562	blood:
11	chr19:39304217..39307847-chr19:39338556..39341715,3	MCF-7	breast:
12	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
13	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
14	chr19:39338392..39342144-chr19:39367920..39369868,4	K562	blood:
15	chr19:39108186..39111004-chr19:39340137..39342268,2	K562	blood:
16	chr19:39338470..39342492-chr19:39367140..39370147,4	K562	blood:
17	chr11:67069791..67071479-chr19:39339670..39341309,2	MCF-7	breast:
18	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
19	chr19:39341057..39343314-chr19:39902630..39904241,2	MCF-7	breast:
20	chr19:39226722..39228357-chr19:39340194..39343791,3	K562	blood:
21	chr19:39339873..39342860-chr19:39409643..39412054,2	MCF-7	breast:
22	chr19:39233778..39236095-chr19:39340274..39342606,2	K562	blood:
23	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:
24	chr19:39224740..39226667-chr19:39338777..39342180,3	K562	blood:
25	chr19:39340592..39344706-chr19:39357882..39361932,6	K562	blood:
26	chr19:39340110..39342981-chr19:39406423..39409674,4	MCF-7	breast:
27	chr19:39339112..39343595-chr19:39368855..39373078,6	MCF-7	breast:
28	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
29	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:
30	chr19:39137047..39143767-chr19:39341076..39344906,12	MCF-7	breast:
31	chr19:39338733..39343337-chr19:39388774..39392675,12	K562	blood:
32	chr19:39339114..39344809-chr19:39363672..39368217,5	MCF-7	breast:
33	chr19:39026179..39027940-chr19:39341068..39343027,2	MCF-7	breast:
34	chr19:39339767..39341589-chr19:39404601..39407841,3	K562	blood:
35	chr19:39340906..39344724-chr19:39389015..39390874,4	MCF-7	breast:
36	chr19:39339409..39344372-chr19:39356868..39363816,11	MCF-7	breast:
37	chr19:39200022..39202960-chr19:39340126..39342618,2	K562	blood:
38	chr19:1249375..1249892-chr19:39340631..39341416,2	Hela-S3	cervix:
39	chr19:39108057..39110372-chr19:39339414..39342268,3	K562	blood:
40	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
41	chr19:39340477..39342745-chr7:150775717..150778073,2	MCF-7	breast:
42	chr19:39340089..39343125-chr19:39404601..39408323,3	K562	blood:

Variant related genes	Relation type
HNRNPL	TF binding region
ENSG00000090924	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000164896	Chromatin interaction
ENSG00000167470	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000269190	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000096968	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000172830	Chromatin interaction
ENSG00000268055	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 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
9	esv1792093	chr19:39339989-39341182	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	n/a
10	esv1796413	chr19:39339989-39341182	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	n/a
11	esv1797170	chr19:39339989-39341182	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	n/a
12	esv1799902	chr19:39339989-39341182	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	n/a
13	esv1801586	chr19:39339989-39341182	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	n/a
14	esv1802369	chr19:39339989-39341182	Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	n/a
15	esv1834918	chr19:39339989-39341182	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' 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	chr19:39338600-39341600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:39338600-39343800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:39338800-39341400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:39338800-39341600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:39338800-39343400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:39339000-39341400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:39339000-39341800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:39339000-39344000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:39339200-39341400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:39339200-39343400	Active TSS	Esophagus	oesophagus
11	chr19:39339400-39341400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:39339400-39341400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:39339400-39341400	Active TSS	HMEC	breast
14	chr19:39339400-39341600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:39339400-39341600	Active TSS	Placenta Amnion	Placenta Amnion
16	chr19:39339400-39341600	Active TSS	HSMMtube	muscle
17	chr19:39339400-39341800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr19:39339400-39342000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:39339600-39341400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:39339600-39341400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:39339600-39341400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:39339600-39341400	Active TSS	Fetal Muscle Trunk	muscle
23	chr19:39339600-39341400	Active TSS	Placenta	Placenta
24	chr19:39339600-39341400	Active TSS	Rectal Smooth Muscle	rectum
25	chr19:39339600-39341400	Active TSS	HSMM	muscle
26	chr19:39339600-39341400	Active TSS	NHLF	lung
27	chr19:39339600-39341600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:39339600-39341600	Active TSS	Brain Germinal Matrix	brain
29	chr19:39339600-39341600	Active TSS	Colonic Mucosa	Colon
30	chr19:39339600-39343200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr19:39339800-39341400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:39339800-39341400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:39339800-39341400	Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr19:39339800-39341400	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr19:39339800-39341400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:39339800-39341400	Active TSS	Muscle Satellite Cultured Cells	--
37	chr19:39339800-39341400	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr19:39339800-39341400	Active TSS	Duodenum Mucosa	Duodenum
39	chr19:39339800-39341400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr19:39339800-39341400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr19:39339800-39341400	Active TSS	Fetal Brain Female	brain
42	chr19:39339800-39341400	Weak transcription	Fetal Heart	heart
43	chr19:39339800-39341400	Active TSS	Fetal Intestine Large	intestine
44	chr19:39339800-39341400	Active TSS	Fetal Muscle Leg	muscle
45	chr19:39339800-39341400	Active TSS	Fetal Thymus	thymus
46	chr19:39339800-39341400	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr19:39339800-39341400	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr19:39339800-39341400	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr19:39339800-39341400	Active TSS	Stomach Smooth Muscle	stomach
50	chr19:39339800-39341400	Active TSS	A549	lung

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