Variant report

Variant	rs2075282
Chromosome Location	chr19:38308774-38308775
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr19:38307632-38308820	SK-N-SH	brain:	n/a	chr19:38308217-38308226
2	REST	chr19:38307930-38308908	H1-neurons	neurons:	n/a	chr19:38308320-38308330

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38308749-38308799	HAEpiC	amniotic membrane:	n/a
2	chr19:38308749-38308799	Hela-S3	cervix:	n/a
3	chr19:38308749-38308799	CMK	blood:	n/a
4	chr19:38308749-38308799	A549	lung:	n/a
5	chr19:38308749-38308799	AG09319	gingival:	n/a
6	chr19:38308749-38308799	NHBE	bronchial:	n/a
7	chr19:38308749-38308799	BE2_C	brain:	n/a
8	chr19:38308749-38308799	HEK293	kidney:	embryo
9	chr19:38308749-38308799	BJ	skin:	n/a
10	chr19:38308749-38308799	HCT-116	colon:	n/a
11	chr19:38308749-38308799	HNPCEpiC	eye:	n/a
12	chr19:38308749-38308799	HUVEC	blood vessel:	n/a
13	chr19:38308749-38308799	Hepatocyte	liver:	n/a
14	chr19:38308749-38308799	SKMC	muscle:	n/a
15	chr19:38308749-38308799	Jurkat	blood:	n/a
16	chr19:38308749-38308799	SK-N-MC	brain:	n/a
17	chr19:38308749-38308799	RPTEC	kidney:	n/a
18	chr19:38308749-38308799	AG04449	skin:	fetal
19	chr19:38308749-38308799	AG09309	skin:	n/a
20	chr19:38308749-38308799	T-47D	breast:	n/a
21	chr19:38308749-38308799	ECC-1	luminal epithelium:	n/a
22	chr19:38308749-38308799	HepG2	liver:	n/a
23	chr19:38308749-38308799	NT2-D1	testis:	n/a
24	chr19:38308749-38308799	NB4	blood:	n/a
25	chr19:38308749-38308799	HL-60	blood:	n/a
26	chr19:38308749-38308799	HRE	kidney:	n/a
27	chr19:38308749-38308799	GM19239	blood:	n/a
28	chr19:38308749-38308799	LNCaP	prostate:	n/a
29	chr19:38308749-38308799	H1-hESC	embryonic stem cell:	embryo
30	chr19:38308749-38308799	HRCEpiC	kidney:	n/a
31	chr19:38308749-38308799	GM06990	blood:	n/a
32	chr19:38308749-38308799	AG04450	lung:	fetal
33	chr19:38308749-38308799	HCPEpiC	choroid plexus:	n/a
34	chr19:38308749-38308799	HEEpiC	esophagus:	n/a
35	chr19:38308749-38308799	AoSMC	blood vessel:	n/a
36	chr19:38308749-38308799	U87	brain:	n/a
37	chr19:38308749-38308799	HCF	heart:	n/a
38	chr19:38308749-38308799	MCF-7	breast:	n/a
39	chr19:38308749-38308799	Caco-2	colon:	n/a
40	chr19:38308749-38308799	GM12878	blood:	n/a
41	chr19:38308749-38308799	PFSK-1	brain:	n/a
42	chr19:38308749-38308799	SK-N-SH_RA	brain:	n/a
43	chr19:38308749-38308799	HIPEpiC	eye:	n/a
44	chr19:38308749-38308799	HCM	heart:	n/a
45	chr19:38308749-38308799	HRPEpiC	eye:	n/a
46	chr19:38308749-38308799	MCF10A-Er-Src	breast:	n/a
47	chr19:38308749-38308799	PANC-1	pancreas:	n/a
48	chr19:38308749-38308799	AG10803	skin:	n/a
49	chr19:38308749-38308799	HMEC	breast:	n/a
50	chr19:38308749-38308799	GM12892	blood:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L3-3	chr19:38308566-38308782	ENSG00000267640.1

No data

Variant related genes	Relation type
ZNF573	TF binding region
ZNF573	CpG island

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11880056	1.00[JPT][hapmap]
rs11883255	1.00[JPT][hapmap]
rs35714505	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7245981	1.00[JPT][hapmap]
rs73031218	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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38307200-38308800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr19:38307200-38308800	ZNF genes & repeats	Esophagus	oesophagus
3	chr19:38307400-38308800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr19:38307400-38308800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:38307400-38308800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr19:38307400-38308800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
7	chr19:38307400-38308800	ZNF genes & repeats	Liver	Liver
8	chr19:38307400-38308800	Active TSS	Fetal Kidney	kidney
9	chr19:38307400-38308800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:38307400-38308800	ZNF genes & repeats	NHEK	skin
11	chr19:38307400-38309000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:38307400-38309000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:38307400-38309000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:38307400-38309000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr19:38307400-38309400	ZNF genes & repeats	Placenta	Placenta
16	chr19:38307600-38308800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38307600-38308800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:38307600-38308800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:38307600-38308800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:38307600-38308800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
21	chr19:38307600-38308800	ZNF genes & repeats	Primary T cells from cord blood	blood
22	chr19:38307600-38308800	Active TSS	Duodenum Mucosa	Duodenum
23	chr19:38307600-38308800	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:38307600-38308800	Active TSS	Left Ventricle	heart
25	chr19:38307600-38308800	Active TSS	Right Atrium	heart
26	chr19:38307600-38308800	Active TSS	NHDF-Ad	bronchial
27	chr19:38307600-38308800	Active TSS	Osteobl	bone
28	chr19:38307600-38309000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr19:38307600-38309000	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr19:38307600-38309000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:38307600-38309000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr19:38307600-38309000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:38307600-38309000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:38307800-38308800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr19:38307800-38308800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr19:38307800-38308800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:38307800-38308800	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr19:38307800-38308800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:38307800-38308800	Active TSS	Colon Smooth Muscle	Colon
40	chr19:38307800-38308800	Active TSS	Fetal Heart	heart
41	chr19:38307800-38308800	Active TSS	Fetal Intestine Small	intestine
42	chr19:38307800-38308800	ZNF genes & repeats	Fetal Thymus	thymus
43	chr19:38307800-38308800	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr19:38307800-38308800	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr19:38307800-38308800	Active TSS	Right Ventricle	heart
46	chr19:38307800-38308800	ZNF genes & repeats	HMEC	breast
47	chr19:38308000-38308800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:38308000-38309600	Active TSS	Fetal Brain Male	brain
49	chr19:38308200-38308800	Flanking Active TSS	Ovary	ovary
50	chr19:38308200-38308800	Active TSS	Psoas Muscle	Psoas

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