Variant report

Variant	rs3786872
Chromosome Location	chr19:38756089-38756090
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38753791..38756428-chr19:38824915..38829046,7	MCF-7	breast:
2	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
3	chr19:38753833..38757251-chr19:38808796..38812283,9	MCF-7	breast:
4	chr19:38714374..38716736-chr19:38753965..38756092,2	MCF-7	breast:
5	chr19:38755064..38756730-chr19:38799714..38801909,2	MCF-7	breast:
6	chr19:38753863..38756169-chr22:39637561..39639361,2	MCF-7	breast:
7	chr19:38752235..38756779-chr19:38783718..38786830,7	MCF-7	breast:
8	chr19:38755112..38757929-chr19:38851639..38853560,2	MCF-7	breast:
9	chr19:38746268..38748708-chr19:38755363..38757878,2	K562	blood:
10	chr19:38753926..38756538-chr19:38833889..38836607,2	MCF-7	breast:
11	chr19:38755234..38758154-chr19:38804246..38806924,3	K562	blood:
12	chr19:38755242..38758154-chr19:38804246..38806924,2	K562	blood:
13	chr19:38718052..38720655-chr19:38755234..38758069,2	MCF-7	breast:
14	chr19:36629466..36631434-chr19:38753724..38756328,2	MCF-7	breast:
15	chr19:38746268..38750016-chr19:38754499..38757878,4	K562	blood:
16	chr19:38753341..38760825-chr19:38779856..38783291,10	MCF-7	breast:
17	chr19:38755353..38758137-chr19:38878117..38880491,3	MCF-7	breast:
18	chr19:38753811..38757692-chr19:38863788..38867160,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000179168	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000200209	Chromatin interaction
ENSG00000100311	Chromatin interaction
ENSG00000099337	Chromatin interaction
ENSG00000167644	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12610791	0.86[CHD][hapmap]
rs12981507	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35946591	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71337551	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3786872	PSG3	cis	parietal	SCAN
rs3786872	C19orf33	cis	multi-tissue	Pritchard
rs3786872	SPINT2	cis	lymphoblastoid	seeQTL
rs3786872	TEX101	cis	parietal	SCAN
rs3786872	PPP1R14A	cis	multi-tissue	Pritchard
rs3786872	OPA3	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38754200-38757000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr19:38754200-38757000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:38754400-38756200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:38754400-38756200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr19:38754400-38756400	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr19:38754400-38756600	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr19:38754400-38756600	Active TSS	Aorta	Aorta
8	chr19:38754400-38756600	Active TSS	Brain Cingulate Gyrus	brain
9	chr19:38754400-38756600	Active TSS	Pancreas	Pancrea
10	chr19:38754400-38756800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:38754400-38756800	Active TSS	Brain Angular Gyrus	brain
12	chr19:38754400-38756800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr19:38754600-38756200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:38754600-38756200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr19:38754600-38756400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr19:38754600-38756600	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:38754600-38756600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:38754600-38756600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr19:38754600-38759000	Active TSS	Rectal Smooth Muscle	rectum
20	chr19:38754800-38756200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:38754800-38756200	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:38754800-38756200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:38754800-38756400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:38754800-38756400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:38754800-38756400	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr19:38754800-38756400	Active TSS	Duodenum Mucosa	Duodenum
27	chr19:38754800-38756600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:38754800-38756800	Active TSS	Gastric	stomach
29	chr19:38754800-38756800	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr19:38754800-38757000	Active TSS	Fetal Kidney	kidney
31	chr19:38754800-38757200	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr19:38754800-38757800	Active TSS	Small Intestine	intestine
33	chr19:38754800-38758400	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr19:38755000-38756200	Active TSS	H1 Cell Line	embryonic stem cell
35	chr19:38755000-38756200	Enhancers	Fetal Heart	heart
36	chr19:38755000-38756200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr19:38755000-38756400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:38755000-38756600	Active TSS	Colon Smooth Muscle	Colon
39	chr19:38755000-38756600	Active TSS	Fetal Intestine Small	intestine
40	chr19:38755000-38756800	Active TSS	Fetal Intestine Large	intestine
41	chr19:38755000-38756800	Bivalent/Poised TSS	Fetal Stomach	stomach
42	chr19:38755000-38757000	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr19:38755000-38757200	Active TSS	NHEK	skin
44	chr19:38755000-38757400	Active TSS	HMEC	breast
45	chr19:38755200-38756200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:38755200-38756200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:38755200-38756400	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr19:38755200-38756400	Active TSS	Stomach Mucosa	stomach
49	chr19:38755200-38756600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr19:38755200-38756600	Flanking Active TSS	Thymus	Thymus

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