Variant report

Variant	rs184239
Chromosome Location	chr19:44084155-44084156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr19:44084133-44084734	GM12878	blood:	n/a	n/a
2	NFATC1	chr19:44084119-44084461	GM12878	blood:	n/a	n/a
3	JUND	chr19:44083900-44086327	SK-N-SH	brain:	n/a	chr19:44084081-44084088
4	POLR2A	chr19:44083975-44085128	H1-hESC	embryonic stem cell:	n/a	n/a
5	STAT5A	chr19:44084093-44084547	GM12878	blood:	n/a	chr19:44084394-44084406 chr19:44084272-44084284
6	PML	chr19:44084067-44084920	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44082737..44084299-chr19:44149174..44151871,2	MCF-7	breast:
2	chr19:44082767..44086072-chr19:44097414..44100193,3	MCF-7	breast:
3	chr19:44083278..44085752-chr19:44098903..44101247,2	MCF-7	breast:
4	chr19:44082516..44084852-chr19:44122314..44123953,3	K562	blood:
5	chr19:44078955..44081902-chr19:44082644..44085623,4	MCF-7	breast:
6	chr19:44079920..44081896-chr19:44082367..44084716,3	K562	blood:
7	chr19:44079733..44081896-chr19:44082367..44084669,4	K562	blood:
8	chr19:44082536..44084852-chr19:44121728..44123814,2	K562	blood:
9	chr19:44082364..44084378-chr19:44084508..44086899,2	K562	blood:

No data

Variant related genes	Relation type
PINLYP	TF binding region
XRCC1	TF binding region
ENSG00000124444	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000234465	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000226763	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10402946	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs12973764	0.89[CEU][hapmap]
rs12979907	0.81[EUR][1000 genomes]
rs12980646	0.94[CEU][hapmap]
rs12981023	0.88[CEU][hapmap]
rs12981701	0.80[ASN][1000 genomes]
rs12983281	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1475933	0.83[ASN][1000 genomes]
rs17655646	1.00[CHB][hapmap]
rs1978008	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2030404	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs2102954	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2139720	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs25479	0.83[ASN][1000 genomes]
rs25485	0.81[ASN][1000 genomes]
rs2599462	0.87[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2682563	0.87[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2682585	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2854500	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854501	0.91[ASW][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854506	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2854507	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2854508	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2854509	0.93[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs304731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213255	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3213263	0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3213276	0.98[ASN][1000 genomes]
rs3213295	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3213329	0.83[ASN][1000 genomes]
rs3213333	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3213334	0.92[ASW][hapmap];0.85[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3213356	0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3213387	0.83[ASN][1000 genomes]
rs34704825	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34977009	0.81[EUR][1000 genomes]
rs35016410	0.81[EUR][1000 genomes]
rs3547	0.83[ASN][1000 genomes]
rs35485252	0.82[EUR][1000 genomes]
rs36075334	0.82[EUR][1000 genomes]
rs3810381	0.81[EUR][1000 genomes]
rs4507015	0.81[EUR][1000 genomes]
rs4544340	0.81[EUR][1000 genomes]
rs4802183	0.89[CEU][hapmap]
rs4802185	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs4803646	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs56012842	0.80[EUR][1000 genomes]
rs6509094	0.82[EUR][1000 genomes]
rs71362654	0.81[EUR][1000 genomes]
rs7248927	0.82[EUR][1000 genomes]
rs7251275	1.00[CHB][hapmap]
rs7252962	0.81[EUR][1000 genomes]
rs7253177	0.81[EUR][1000 genomes]
rs7253856	0.83[CEU][hapmap]
rs73043690	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs762506	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762507	0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8100211	0.82[EUR][1000 genomes]
rs915927	0.81[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	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs184239	ELSPBP1	cis	cerebellum	SCAN
rs184239	BLOC1S3	cis	parietal	SCAN
rs184239	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs184239	ETHE1	cis	lymphoblastoid	seeQTL
rs184239	XRCC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44079800-44085400	Weak transcription	Gastric	stomach
2	chr19:44079800-44098200	Weak transcription	Small Intestine	intestine
3	chr19:44080400-44084200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:44080400-44084200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:44080400-44084200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:44080400-44084200	Weak transcription	Liver	Liver
7	chr19:44080400-44084200	Weak transcription	Left Ventricle	heart
8	chr19:44080400-44084200	Weak transcription	Lung	lung
9	chr19:44080400-44084200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:44080400-44084200	Weak transcription	Right Atrium	heart
11	chr19:44080400-44084200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr19:44080400-44084200	Weak transcription	HUVEC	blood vessel
13	chr19:44080400-44090200	Weak transcription	HSMM	muscle
14	chr19:44080600-44084200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:44080600-44084200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr19:44080600-44084200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:44080600-44084200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:44080600-44084200	Weak transcription	Right Ventricle	heart
19	chr19:44080600-44084400	Weak transcription	Spleen	Spleen
20	chr19:44080600-44090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:44080600-44095600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:44080800-44084200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr19:44080800-44088400	Weak transcription	A549	lung
24	chr19:44081000-44084200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:44081000-44084200	Weak transcription	Esophagus	oesophagus
26	chr19:44081000-44084200	Weak transcription	Fetal Heart	heart
27	chr19:44081000-44084200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:44081000-44085200	Weak transcription	Pancreas	Pancrea
29	chr19:44081400-44090200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:44081400-44090200	Weak transcription	NHEK	skin
31	chr19:44081600-44090600	Weak transcription	HMEC	breast
32	chr19:44083000-44084200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:44083000-44087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:44083800-44084200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr19:44083800-44084200	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr19:44083800-44084200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:44083800-44084200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:44083800-44084200	Enhancers	Fetal Brain Male	brain
39	chr19:44083800-44084200	Flanking Active TSS	Thymus	Thymus
40	chr19:44083800-44084400	Flanking Active TSS	Fetal Lung	lung
41	chr19:44083800-44084400	Flanking Active TSS	Fetal Thymus	thymus
42	chr19:44083800-44084600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr19:44083800-44085200	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr19:44083800-44085200	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr19:44083800-44085200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:44083800-44085200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:44083800-44085200	Active TSS	Fetal Brain Female	brain
48	chr19:44083800-44085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:44083800-44085600	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr19:44083800-44085800	Active TSS	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links