Variant report

Variant	rs2356549
Chromosome Location	chr19:44511202-44511203
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44506934..44508722-chr19:44508906..44511281,4	K562	blood:
2	chr19:44438985..44440520-chr19:44510451..44513064,2	MCF-7	breast:
3	chr19:44506929..44508722-chr19:44508906..44512991,6	K562	blood:
4	chr19:44510545..44512229-chr19:44575902..44577637,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186026	Chromatin interaction
ENSG00000124459	Chromatin interaction
ENSG00000266921	Chromatin interaction
ENSG00000159882	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10418363	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083732	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083733	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11881151	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12232810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1996408	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2191566	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270196	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35292176	0.84[EUR][1000 genomes]
rs367209	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367499	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs369106	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs377503	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810406	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs384544	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs390369	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4433920	0.80[ASN][1000 genomes]
rs4482396	0.82[ASN][1000 genomes]
rs4803667	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803669	0.87[ASN][1000 genomes]
rs4803675	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs55703004	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56101767	0.91[EUR][1000 genomes]
rs56171514	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56317065	0.85[ASN][1000 genomes]
rs59963278	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62115482	0.83[ASN][1000 genomes]
rs62115484	0.81[ASN][1000 genomes]
rs62119173	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62119176	0.90[ASN][1000 genomes]
rs6509133	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509138	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7245749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252394	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253205	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254261	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs7254907	0.82[ASN][1000 genomes]
rs7255145	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255512	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7256908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258517	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7260075	0.80[ASN][1000 genomes]
rs73037629	0.83[ASN][1000 genomes]
rs8104605	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs8105571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2356549	HIF3A	cis	parietal	SCAN
rs2356549	OPA3	cis	cerebellum	SCAN
rs2356549	FOXA3	cis	cerebellum	SCAN
rs2356549	ZNF155	cis	multi-tissue	Pritchard
rs2356549	ZNF223	cis	Thyroid	GTEx
rs2356549	OPA3	cis	parietal	SCAN
rs2356549	CCDC114	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44508000-44511600	Weak transcription	Pancreas	Pancrea
2	chr19:44508200-44511400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:44508200-44511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:44508200-44511600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:44508200-44511600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:44508200-44511600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:44508200-44511800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:44508200-44511800	Weak transcription	Stomach Mucosa	stomach
9	chr19:44508200-44512000	Weak transcription	HSMM	muscle
10	chr19:44508200-44512800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:44508400-44511400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:44508400-44511400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:44508400-44511400	Weak transcription	Fetal Brain Male	brain
14	chr19:44508400-44511400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:44508400-44511400	Weak transcription	Fetal Thymus	thymus
16	chr19:44508400-44511400	Weak transcription	Right Ventricle	heart
17	chr19:44508400-44511400	Weak transcription	NH-A	brain
18	chr19:44508400-44511600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:44508400-44511600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:44508400-44511600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:44508400-44511600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:44508400-44511600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:44508400-44511600	Weak transcription	Fetal Stomach	stomach
24	chr19:44508400-44511600	Weak transcription	HepG2	liver
25	chr19:44508400-44511600	Weak transcription	NHEK	skin
26	chr19:44508400-44511600	Weak transcription	NHLF	lung
27	chr19:44508400-44511800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:44508400-44512000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:44508400-44512000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr19:44508400-44512000	Weak transcription	HSMMtube	muscle
31	chr19:44508400-44512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:44508400-44512200	Weak transcription	HMEC	breast
33	chr19:44508400-44512800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:44508400-44513000	Weak transcription	K562	blood
35	chr19:44508400-44513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:44508400-44513600	Weak transcription	Hela-S3	cervix
37	chr19:44508600-44512600	Weak transcription	NHDF-Ad	bronchial
38	chr19:44509200-44520600	ZNF genes & repeats	Liver	Liver
39	chr19:44509400-44516800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr19:44509400-44518200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:44509800-44516600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr19:44509800-44517000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:44509800-44517400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
44	chr19:44510000-44517000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
45	chr19:44510000-44517000	ZNF genes & repeats	Adipose Nuclei	Adipose
46	chr19:44510000-44517200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr19:44510000-44517400	ZNF genes & repeats	Primary T cells from cord blood	blood
48	chr19:44510200-44512000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:44510200-44513000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:44510200-44516600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood

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