Variant report

Variant	rs2040562
Chromosome Location	chr19:19248107-19248108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr19:19247769-19248145	K562	blood:	n/a	n/a
2	POLR2A	chr19:19247581-19249565	K562	blood:	n/a	n/a
3	POLR2A	chr19:19247661-19248219	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr19:19247736-19249446	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19229745..19232931-chr19:19245473..19249545,7	K562	blood:
2	chr19:19142872..19145120-chr19:19247673..19249634,2	K562	blood:
3	chr19:19172595..19175925-chr19:19247411..19251399,4	MCF-7	breast:
4	chr19:19245624..19248582-chr19:19303054..19304930,2	K562	blood:
5	chr19:19246857..19248644-chr19:19456202..19457760,2	K562	blood:
6	chr19:19153988..19156786-chr19:19246941..19248675,2	K562	blood:
7	chr19:19163080..19165123-chr19:19247773..19249964,2	MCF-7	breast:
8	chr19:19229446..19234006-chr19:19241302..19251526,15	K562	blood:
9	chr19:19169646..19176667-chr19:19241603..19249514,19	K562	blood:
10	chr19:19216253..19217808-chr19:19246400..19248362,2	K562	blood:
11	chr19:19169646..19176603-chr19:19241603..19250623,23	K562	blood:
12	chr19:19187730..19190152-chr19:19246123..19249004,2	K562	blood:

No data

Variant related genes	Relation type
TMEM161A	TF binding region
ENSG00000064607	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000064545	Chromatin interaction
ENSG00000181035	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10414676	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2040561	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826993	0.91[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4808924	0.81[EUR][1000 genomes]
rs6511020	0.82[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6511021	0.86[TSI][hapmap];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2040562	ZNF506	cis	parietal	SCAN
rs2040562	TMEM161A	cis	Muscle Skeletal	GTEx
rs2040562	MED26	cis	parietal	SCAN
rs2040562	ZNF93	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19180600-19248400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr19:19222200-19248200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:19230800-19248400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:19243400-19248200	Weak transcription	Fetal Brain Female	brain
5	chr19:19243400-19248200	Weak transcription	Fetal Lung	lung
6	chr19:19243600-19248200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr19:19243600-19248200	Weak transcription	Colonic Mucosa	Colon
8	chr19:19243600-19248400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:19243600-19248400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:19243600-19248400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:19243800-19248200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:19243800-19248200	Weak transcription	Primary T cells from cord blood	blood
13	chr19:19243800-19248200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:19243800-19248200	Weak transcription	HSMMtube	muscle
15	chr19:19243800-19248600	Weak transcription	Aorta	Aorta
16	chr19:19244200-19248400	Weak transcription	A549	lung
17	chr19:19245400-19248600	Weak transcription	Fetal Kidney	kidney
18	chr19:19245600-19248400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:19245800-19248200	Weak transcription	HMEC	breast
20	chr19:19245800-19248400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr19:19246000-19248200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:19246000-19248200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:19246000-19248200	Weak transcription	Fetal Heart	heart
24	chr19:19246000-19248200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr19:19246000-19248600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:19246200-19248200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:19246200-19248200	Weak transcription	Brain Germinal Matrix	brain
28	chr19:19246200-19248400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:19246200-19248400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:19246200-19248600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:19247600-19248200	Enhancers	Fetal Muscle Leg	muscle
32	chr19:19247600-19248400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:19247800-19248200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:19247800-19248200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:19247800-19248200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:19247800-19248200	Enhancers	Brain Anterior Caudate	brain
37	chr19:19247800-19248200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr19:19247800-19248200	Enhancers	Stomach Mucosa	stomach
39	chr19:19247800-19248400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:19247800-19248400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:19247800-19248400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr19:19247800-19248400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr19:19247800-19248400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr19:19247800-19248400	Enhancers	Liver	Liver
45	chr19:19247800-19248400	Enhancers	Esophagus	oesophagus
46	chr19:19247800-19248400	Enhancers	Gastric	stomach
47	chr19:19247800-19248400	Enhancers	Ovary	ovary
48	chr19:19247800-19248400	Enhancers	Pancreas	Pancrea
49	chr19:19247800-19248400	Enhancers	Right Atrium	heart
50	chr19:19247800-19248400	Enhancers	Right Ventricle	heart

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