Variant report

Variant	rs2657924
Chromosome Location	chr19:52777449-52777450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:52777411-52778081	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:52777372-52778052	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:52777431-52777874	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:52777289-52778005	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:52777415-52777874	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:
2	chr19:52776723..52778376-chr19:52800239..52801922,2	K562	blood:

Variant related genes	Relation type
ZNF766	TF binding region
ENSG00000198464	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10404635	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10425462	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10425644	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2089275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560871	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560873	0.85[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560875	0.81[AFR][1000 genomes]
rs2560877	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657926	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657928	0.81[AFR][1000 genomes]
rs2657930	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28718737	0.81[ASN][1000 genomes]
rs56211703	0.96[ASN][1000 genomes]
rs56369375	0.90[ASN][1000 genomes]
rs62110397	1.00[ASN][1000 genomes]
rs62110398	1.00[ASN][1000 genomes]
rs7255504	0.90[ASN][1000 genomes]
rs8107325	1.00[ASN][1000 genomes]
rs8113537	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9304726	0.84[CHB][hapmap];0.90[ASN][1000 genomes]
rs9304727	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2657924	ZNF582	cis	parietal	SCAN
rs2657924	LAIR1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774000-52780000	Weak transcription	Aorta	Aorta
2	chr19:52774000-52780200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:52774000-52786600	Weak transcription	Right Ventricle	heart
4	chr19:52774000-52787200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:52774200-52786600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
8	chr19:52774400-52777600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:52774400-52777800	ZNF genes & repeats	A549	lung
10	chr19:52774400-52778400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:52774400-52778400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
12	chr19:52774400-52779200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:52774400-52781000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:52774400-52782000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:52774400-52786600	Weak transcription	Osteobl	bone
16	chr19:52774400-52787000	Weak transcription	HUVEC	blood vessel
17	chr19:52774400-52787400	Weak transcription	NHDF-Ad	bronchial
18	chr19:52774600-52777600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:52774600-52777800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr19:52774600-52777800	ZNF genes & repeats	Fetal Thymus	thymus
21	chr19:52774600-52778600	ZNF genes & repeats	Thymus	Thymus
22	chr19:52774600-52780000	Weak transcription	Colonic Mucosa	Colon
23	chr19:52774600-52780400	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr19:52774600-52781200	ZNF genes & repeats	GM12878-XiMat	blood
25	chr19:52774600-52782000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:52774600-52782600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:52774600-52783600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:52774600-52783800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
29	chr19:52774600-52786400	Weak transcription	Brain Angular Gyrus	brain
30	chr19:52774600-52786600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:52774600-52795800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr19:52774800-52777600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:52774800-52777800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr19:52774800-52777800	Genic enhancers	Dnd41	blood
35	chr19:52774800-52778000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:52774800-52779800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:52774800-52780400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr19:52774800-52782400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:52774800-52786400	Weak transcription	Brain Substantia Nigra	brain
40	chr19:52775000-52777800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:52775000-52778000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:52775000-52785400	Weak transcription	Gastric	stomach
43	chr19:52775000-52786400	Weak transcription	Brain Hippocampus Middle	brain
44	chr19:52775000-52786400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:52775000-52787400	Weak transcription	HepG2	liver
46	chr19:52775200-52777600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:52775200-52778000	Strong transcription	Fetal Lung	lung
48	chr19:52775200-52786600	Weak transcription	Left Ventricle	heart
49	chr19:52775400-52777600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
50	chr19:52775400-52777800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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