Variant report

Variant	rs4283339
Chromosome Location	chr19:55769454-55769455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr19:55768656-55771041	K562	blood:	n/a	n/a
2	SIN3AK20	chr19:55768209-55771137	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:55769363-55769804	GM12878	blood:	n/a	n/a
4	REST	chr19:55769162-55771383	H1-neurons	neurons:	n/a	chr19:55769581-55769594 chr19:55769348-55769368
5	POLR2A	chr19:55768453-55769545	GM12878	blood:	n/a	n/a
6	ELF1	chr19:55768714-55771361	GM12878	blood:	n/a	chr19:55769295-55769304 chr19:55770446-55770458 chr19:55770320-55770332 chr19:55770073-55770085 chr19:55769296-55769308 chr19:55770333-55770345
7	RAD21	chr19:55769357-55769598	IMR90	lung:	n/a	n/a
8	BHLHE40	chr19:55768690-55769575	GM12878	blood:	n/a	n/a
9	NRF1	chr19:55769266-55771044	SK-N-SH	brain:	n/a	chr19:55770536-55770547 chr19:55770476-55770490 chr19:55770449-55770458 chr19:55770536-55770547 chr19:55770434-55770448 chr19:55770479-55770490
10	ZBTB7A	chr19:55769440-55770917	K562	blood:	n/a	n/a
11	ZBTB7A	chr19:55769153-55770948	K562	blood:	n/a	n/a
12	HCFC1	chr19:55769257-55771331	Hela-S3	cervix:	n/a	n/a
13	SMARCB1	chr19:55768503-55771011	Hela-S3	cervix:	n/a	n/a
14	MAX	chr19:55767994-55769837	K562	blood:	n/a	chr19:55769750-55769759 chr19:55768523-55768532
15	MAZ	chr19:55768682-55771570	IMR90	lung:	n/a	chr19:55770411-55770421 chr19:55769750-55769759
16	WRNIP1	chr19:55764368-55769616	GM12878	blood:	n/a	n/a
17	MAZ	chr19:55768527-55771142	GM12878	blood:	n/a	chr19:55770411-55770421 chr19:55769750-55769759
18	RCOR1	chr19:55768381-55771561	IMR90	lung:	n/a	n/a
19	MXI1	chr19:55768383-55771353	IMR90	lung:	n/a	n/a
20	SIN3AK20	chr19:55769415-55770141	K562	blood:	n/a	n/a
21	UBTF	chr19:55769144-55769621	K562	blood:	n/a	n/a
22	SIN3AK20	chr19:55768525-55769467	MCF-7	breast:	n/a	n/a
23	SIN3A	chr19:55768749-55769626	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAZ	chr19:55769445-55769565	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:55768786-55769619	MCF-7	breast:	n/a	n/a
26	POLR2A	chr19:55768457-55771612	K562	blood:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55767248..55770437-chr19:55917297..55920206,6	MCF-7	breast:
2	chr19:55768392..55770990-chr19:55864103..55865699,2	MCF-7	breast:
3	chr19:55718690..55723182-chr19:55767265..55771415,7	MCF-7	breast:
4	chr19:55767441..55773483-chr19:55893952..55900251,14	MCF-7	breast:
5	chr19:55690523..55693470-chr19:55767618..55771014,3	K562	blood:
6	chr19:55764902..55773441-chr19:55891413..55900303,21	K562	blood:
7	chr19:55768917..55770461-chr19:55972272..55974611,2	K562	blood:
8	chr19:55763551..55774813-chr19:55891413..55900376,23	K562	blood:
9	chr19:55767441..55772178-chr19:55789060..55793175,7	MCF-7	breast:
10	chr19:55659384..55662186-chr19:55768928..55771825,2	K562	blood:
11	chr19:55768870..55771541-chr19:55794018..55795820,2	MCF-7	breast:
12	chr19:55657829..55659690-chr19:55769331..55772164,2	K562	blood:
13	chr19:55766592..55768703-chr19:55769065..55770634,3	K562	blood:
14	chr19:55767517..55772398-chr19:55789828..55793738,15	K562	blood:
15	chr19:55768444..55771983-chr19:55917721..55920953,5	K562	blood:
16	chr19:55724113..55730012-chr19:55766381..55773608,39	K562	blood:
17	chr19:55690189..55693086-chr19:55769247..55770801,2	MCF-7	breast:
18	chr19:55768912..55770529-chr19:55917802..55919631,2	MCF-7	breast:
19	chr19:55736575..55738793-chr19:55769011..55771822,2	MCF-7	breast:
20	chr19:55750475..55753226-chr19:55768525..55770423,2	MCF-7	breast:
21	chr19:55720878..55730679-chr19:55764402..55774570,47	K562	blood:
22	chr19:55756546..55759225-chr19:55768234..55771187,4	MCF-7	breast:
23	chr19:55769028..55772088-chr19:55788931..55793273,6	MCF-7	breast:
24	chr19:55768430..55771983-chr19:55917442..55920696,5	K562	blood:
25	chr19:55732279..55738678-chr19:55765531..55770516,7	K562	blood:
26	chr19:55767479..55769662-chr19:55951902..55953549,2	MCF-7	breast:
27	chr19:55767450..55771021-chr19:55880319..55882334,3	MCF-7	breast:
28	chr19:55726024..55729916-chr19:55768850..55773519,13	MCF-7	breast:
29	chr19:55764275..55774774-chr19:55790059..55800763,24	K562	blood:

No data

Variant related genes	Relation type
PPP6R1	TF binding region
ENSG00000267649	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000095752	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000269808	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10421676	0.90[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.84[ASN][1000 genomes]
rs11669468	0.85[ASN][1000 genomes]
rs11672947	0.89[ASN][1000 genomes]
rs3786544	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.83[ASN][1000 genomes]
rs62126349	0.87[ASN][1000 genomes]
rs7246293	0.89[ASN][1000 genomes]
rs7257561	0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]

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	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912454	chr19:55725410-55783552	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
6	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
7	nsv912458	chr19:55763409-55823822	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 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	chr19:55764200-55769600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:55764200-55769600	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr19:55764200-55769600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:55764600-55769600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
5	chr19:55764600-55769600	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr19:55764600-55769600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:55764800-55769800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:55764800-55770400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:55765200-55769800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr19:55765400-55769800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr19:55766000-55770600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:55766800-55769800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr19:55767000-55769600	Flanking Active TSS	Colonic Mucosa	Colon
14	chr19:55767800-55769600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:55768000-55769600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:55768200-55769600	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr19:55768200-55769600	Flanking Active TSS	Liver	Liver
18	chr19:55768200-55769600	Flanking Active TSS	Fetal Brain Female	brain
19	chr19:55768200-55771000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:55768400-55769600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr19:55768400-55769600	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr19:55768400-55769600	Flanking Active TSS	Fetal Muscle Trunk	muscle
23	chr19:55768400-55769600	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr19:55768400-55771400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:55768400-55771800	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr19:55768600-55769600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:55768600-55770800	Active TSS	HSMMtube	muscle
28	chr19:55768600-55771000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:55768600-55771200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:55768600-55771200	Active TSS	Ovary	ovary
31	chr19:55768800-55769600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:55768800-55769600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr19:55768800-55769600	Flanking Active TSS	Placenta	Placenta
34	chr19:55768800-55769600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr19:55768800-55770800	Active TSS	Fetal Intestine Small	intestine
36	chr19:55768800-55771000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:55768800-55771000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr19:55768800-55771000	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr19:55768800-55771000	Active TSS	Fetal Intestine Large	intestine
40	chr19:55768800-55771000	Active TSS	Small Intestine	intestine
41	chr19:55768800-55771000	Active TSS	Thymus	Thymus
42	chr19:55768800-55771000	Active TSS	A549	lung
43	chr19:55768800-55771000	Active TSS	GM12878-XiMat	blood
44	chr19:55768800-55771000	Active TSS	K562	blood
45	chr19:55768800-55771000	Active TSS	NHLF	lung
46	chr19:55768800-55771200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:55768800-55771200	Active TSS	Esophagus	oesophagus
48	chr19:55768800-55771200	Active TSS	HSMM	muscle
49	chr19:55768800-55771200	Active TSS	NHDF-Ad	bronchial
50	chr19:55768800-55771400	Active TSS	ES-I3 Cell Line	embryonic stem cell

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