Variant report

Variant	rs56038728
Chromosome Location	chr19:56215850-56215851
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:56215840-56215990	HAc	cerebellar:	n/a	n/a
2	CTCF	chr19:56215800-56215950	A549	lung:	n/a	n/a
3	CTCF	chr19:56215800-56215950	GM12870	blood:	n/a	n/a
4	CTCF	chr19:56215840-56215990	HepG2	liver:	n/a	n/a
5	CTCF	chr19:56215820-56215970	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr19:56215780-56215930	GM12866	blood:	n/a	n/a
7	CTCF	chr19:56215833-56216058	K562	blood:	n/a	n/a
8	CTCF	chr19:56215760-56215910	HFF	foreskin:	n/a	n/a
9	POLR2A	chr19:56214997-56220979	K562	blood:	n/a	n/a
10	CTCF	chr19:56215813-56216032	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:56215794-56216040	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr19:56215820-56215970	HL-60	blood:	n/a	n/a
13	CTCF	chr19:56215847-56215993	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr19:56215840-56215990	AG04449	skin:	n/a	n/a
15	CTCF	chr19:56215840-56215990	BE2_C	brain:	n/a	n/a
16	CTCF	chr19:56215740-56215890	MCF-7	breast:	n/a	n/a
17	CTCF	chr19:56215833-56216057	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:56215160-56217154	SK-N-MC	brain:	n/a	n/a
19	CTCF	chr19:56215820-56215970	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr19:56215840-56215990	GM12871	blood:	n/a	n/a
21	CTCF	chr19:56215780-56215930	GM12868	blood:	n/a	n/a
22	RAD21	chr19:56215806-56216044	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr19:56215790-56216100	K562	blood:	n/a	n/a
24	CTCF	chr19:56215780-56216053	K562	blood:	n/a	n/a
25	CTCF	chr19:56215780-56215930	HEK293	kidney:	n/a	n/a
26	YY1	chr19:56215790-56215987	K562	blood:	n/a	n/a
27	CTCF	chr19:56215820-56215970	GM12864	blood:	n/a	n/a
28	CTCF	chr19:56215840-56215990	HCPEpiC	choroid plexus:	n/a	n/a
29	POLR2A	chr19:56215797-56216557	K562	blood:	n/a	n/a
30	CTCF	chr19:56215840-56215990	GM12872	blood:	n/a	n/a
31	CTCF	chr19:56215732-56216088	K562	blood:	n/a	n/a
32	CTCF	chr19:56215805-56216089	K562	blood:	n/a	n/a
33	POLR2A	chr19:56214868-56217148	PANC-1	pancreas:	n/a	n/a
34	CTCF	chr19:56215800-56215950	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr19:56215755-56216797	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr19:56215797-56217535	GM12891	blood:	n/a	n/a
37	E2F6	chr19:56214913-56216027	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr19:56215837-56216053	HepG2	liver:	n/a	n/a
39	CTCF	chr19:56215820-56215970	GM12865	blood:	n/a	n/a
40	POLR2A	chr19:56215613-56216072	GM12891	blood:	n/a	n/a
41	CTCF	chr19:56215788-56216098	GM12878	blood:	n/a	n/a
42	CTCF	chr19:56215840-56215990	HRPEpiC	eye:	n/a	n/a
43	POLR2A	chr19:56215820-56217054	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr19:56215840-56215990	AG09319	gingival:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56185419..56191490-chr19:56212273..56216664,6	K562	blood:
2	chr19:56214734..56218976-chr19:56219559..56224015,5	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPN1-1	chr19:56215794-56215917	XLOC_013161
2	lnc-EPN1-1	chr19:56215794-56216496	NONHSAT068073

No data

Variant related genes	Relation type
ENSG00000268593	TF binding region
ENSG00000269574	TF binding region
ENSG00000267865	TF binding region
ENSG00000269574	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000267865	Chromatin interaction
ENSG00000063245	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11545669	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs310439	1.00[AFR][1000 genomes]
rs310443	1.00[AFR][1000 genomes]
rs310470	1.00[AFR][1000 genomes]
rs310471	1.00[AFR][1000 genomes]
rs600106	1.00[AFR][1000 genomes]
rs630491	1.00[AFR][1000 genomes]
rs636466	1.00[AFR][1000 genomes]
rs636467	1.00[AFR][1000 genomes]
rs681433	1.00[AFR][1000 genomes]
rs7246799	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
2	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1057383	chr19:56211031-56456028	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56191800-56218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:56195400-56217600	Weak transcription	Right Atrium	heart
4	chr19:56200000-56216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:56202600-56217000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:56206600-56218600	Weak transcription	HepG2	liver
7	chr19:56207000-56219200	Weak transcription	Psoas Muscle	Psoas
8	chr19:56207600-56216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:56207800-56216800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:56208000-56220000	Weak transcription	Fetal Lung	lung
11	chr19:56209000-56217800	Weak transcription	Hela-S3	cervix
12	chr19:56209000-56218000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:56209400-56218200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:56210000-56217800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:56210000-56217800	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:56210000-56218000	Weak transcription	Left Ventricle	heart
17	chr19:56210000-56218400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:56210000-56219600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:56210000-56220000	Weak transcription	Fetal Brain Female	brain
20	chr19:56210200-56216000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:56211200-56218000	Weak transcription	NHEK	skin
22	chr19:56211200-56220800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr19:56212400-56217400	Weak transcription	Thymus	Thymus
24	chr19:56212400-56217600	Weak transcription	Aorta	Aorta
25	chr19:56212400-56217600	Weak transcription	Fetal Muscle Leg	muscle
26	chr19:56212400-56217800	Weak transcription	Brain Germinal Matrix	brain
27	chr19:56212400-56218000	Weak transcription	Brain Anterior Caudate	brain
28	chr19:56212400-56218200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:56212400-56218200	Weak transcription	HMEC	breast
30	chr19:56212400-56218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:56212400-56218400	Weak transcription	Liver	Liver
32	chr19:56212400-56218800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr19:56212400-56219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:56212400-56224000	Weak transcription	HSMM	muscle
35	chr19:56212600-56216200	Weak transcription	Esophagus	oesophagus
36	chr19:56212600-56217600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr19:56212600-56218400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr19:56212600-56218800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:56213000-56216000	Enhancers	Stomach Mucosa	stomach
40	chr19:56213200-56217800	Weak transcription	Primary T cells from cord blood	blood
41	chr19:56213200-56218400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:56213200-56219400	Weak transcription	Adipose Nuclei	Adipose
43	chr19:56214200-56217000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:56214600-56216200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:56214600-56216400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr19:56214600-56216600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr19:56214600-56218000	Weak transcription	K562	blood
48	chr19:56215000-56216200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:56215000-56216400	Strong transcription	Dnd41	blood
50	chr19:56215000-56216600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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