Variant report

Variant	rs2604882
Chromosome Location	chr19:41200511-41200512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41200465-41200636	K562	blood:	n/a	n/a
2	POLR2A	chr19:41200408-41200928	A549	lung:	n/a	n/a
3	POLR2A	chr19:41200288-41200545	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41199688..41201242-chr19:41206885..41209819,2	MCF-7	breast:
2	chr19:41200088..41203329-chr19:41209690..41212303,3	K562	blood:
3	chr19:41193560..41201987-chr19:41206623..41212331,16	K562	blood:
4	chr19:41198980..41204172-chr19:41204698..41209532,5	K562	blood:
5	chr19:41197857..41200529-chr19:41314192..41315970,2	K562	blood:
6	chr19:41145014..41147599-chr19:41198160..41200878,2	K562	blood:
7	chr19:41196517..41199053-chr19:41199774..41203369,4	MCF-7	breast:
8	chr19:41194241..41200533-chr19:41254244..41257966,10	K562	blood:
9	chr19:41198952..41202024-chr19:41219495..41221702,3	MCF-7	breast:
10	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
11	chr19:41200175..41202352-chr19:41204819..41206717,3	MCF-7	breast:

No data

Variant related genes	Relation type
NUMBL	TF binding region
ENSG00000105245	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000188493	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1469427	0.81[ASN][1000 genomes]
rs2115239	0.87[ASN][1000 genomes]
rs2246095	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288451	1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2561535	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2604885	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2604887	0.85[ASN][1000 genomes]
rs3865452	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4802085	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4802086	0.81[JPT][hapmap]
rs4803358	0.87[ASN][1000 genomes]
rs6508944	0.92[ASN][1000 genomes]
rs7257602	0.95[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2604882	IRF2BP1	cis	parietal	SCAN
rs2604882	LIN7B	cis	parietal	SCAN
rs2604882	C19orf54	cis	Nerve Tibial	GTEx
rs2604882	ADCK4	cis	multi-tissue	Pritchard
rs2604882	KCNN4	cis	cerebellum	SCAN
rs2604882	ZNF229	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41197000-41205200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:41197000-41207600	Weak transcription	Fetal Kidney	kidney
3	chr19:41197000-41208000	Weak transcription	Small Intestine	intestine
4	chr19:41197200-41207400	Weak transcription	Stomach Mucosa	stomach
5	chr19:41197200-41210000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:41197200-41210600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:41197200-41220200	Weak transcription	Fetal Heart	heart
8	chr19:41197200-41220600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:41197400-41200800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr19:41197400-41201400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:41197400-41201400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr19:41197400-41202600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr19:41197400-41205200	Weak transcription	Colonic Mucosa	Colon
14	chr19:41197400-41205200	Weak transcription	Osteobl	bone
15	chr19:41197400-41207600	Weak transcription	NHDF-Ad	bronchial
16	chr19:41197400-41210600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:41197400-41219800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:41197400-41220000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr19:41197400-41220000	Strong transcription	Fetal Intestine Small	intestine
20	chr19:41197400-41220200	Weak transcription	HUVEC	blood vessel
21	chr19:41197600-41201200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:41197600-41201600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:41197600-41201800	Weak transcription	HepG2	liver
24	chr19:41197600-41202000	Strong transcription	Liver	Liver
25	chr19:41197600-41202400	Strong transcription	Lung	lung
26	chr19:41197600-41203200	Strong transcription	Spleen	Spleen
27	chr19:41197600-41203400	Strong transcription	Fetal Intestine Large	intestine
28	chr19:41197600-41203600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:41197600-41207000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:41197600-41208800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:41197600-41216000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:41197600-41220200	Weak transcription	Psoas Muscle	Psoas
33	chr19:41197800-41201000	Strong transcription	Esophagus	oesophagus
34	chr19:41197800-41202200	Strong transcription	Placenta	Placenta
35	chr19:41197800-41202200	Strong transcription	Gastric	stomach
36	chr19:41197800-41202400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr19:41197800-41203400	Strong transcription	NHEK	skin
38	chr19:41197800-41203600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:41197800-41203800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:41197800-41204600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:41197800-41205400	Weak transcription	GM12878-XiMat	blood
42	chr19:41197800-41207400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:41197800-41208200	Strong transcription	Fetal Stomach	stomach
44	chr19:41197800-41211000	Weak transcription	Right Atrium	heart
45	chr19:41197800-41219000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr19:41198000-41201400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr19:41198000-41201800	Strong transcription	NHLF	lung
48	chr19:41198000-41203000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:41198000-41203200	Strong transcription	Primary T cells from cord blood	blood
50	chr19:41198000-41203200	Strong transcription	Placenta Amnion	Placenta Amnion

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