Variant report

Variant	rs2311004
Chromosome Location	chr19:36592752-36592753
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36590979..36592787-chr19:36602773..36604776,2	MCF-7	breast:
2	chr19:36592203..36593879-chr19:36596112..36598331,2	K562	blood:
3	chr19:36550207..36552576-chr19:36592409..36594270,2	K562	blood:
4	chr19:36587137..36590524-chr19:36591113..36595249,3	MCF-7	breast:
5	chr19:36580161..36582596-chr19:36590218..36593086,2	MCF-7	breast:
6	chr19:36586278..36587946-chr19:36591359..36594348,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105261	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1003470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420353	0.81[YRI][hapmap]
rs10421966	0.86[YRI][hapmap]
rs10853945	1.00[ASN][1000 genomes]
rs12462674	0.82[YRI][hapmap]
rs12980591	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12982375	0.99[ASN][1000 genomes]
rs1548505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548506	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1972511	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985404	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023865	0.83[YRI][hapmap]
rs2051800	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2072605	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2285745	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2301736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3746271	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826995	0.83[YRI][hapmap]
rs4461192	0.81[YRI][hapmap]
rs4805160	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4806265	0.90[ASN][1000 genomes]
rs4806269	0.95[ASN][1000 genomes]
rs4806270	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510519	0.86[ASN][1000 genomes]
rs7246292	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs757223	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8103569	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2311004	GRIK5	cis	cerebellum	SCAN
rs2311004	CYP2B7P1	cis	parietal	SCAN
rs2311004	ZNF229	cis	parietal	SCAN
rs2311004	ATXN7L1	trans	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
2	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
6	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
7	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:36561200-36597600	Strong transcription	Dnd41	blood
10	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:36561400-36596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr19:36561400-36596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:36563000-36594200	Weak transcription	HSMM	muscle
15	chr19:36568600-36598000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:36568800-36594800	Strong transcription	A549	lung
17	chr19:36568800-36601400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr19:36570000-36598000	Strong transcription	Fetal Thymus	thymus
19	chr19:36571600-36596600	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr19:36571800-36598400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:36571800-36600000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:36571800-36600600	Strong transcription	Fetal Stomach	stomach
23	chr19:36572000-36598000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:36572400-36602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:36573800-36602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:36574200-36593600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr19:36574200-36602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr19:36574600-36604400	Weak transcription	NHDF-Ad	bronchial
29	chr19:36575400-36604200	Weak transcription	Primary B cells from cord blood	blood
30	chr19:36580400-36594800	Weak transcription	Primary T cells from cord blood	blood
31	chr19:36581200-36593600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr19:36581800-36594200	Weak transcription	K562	blood
33	chr19:36583400-36598000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:36583800-36594400	Weak transcription	Placenta	Placenta
35	chr19:36584200-36593800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr19:36584600-36594000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:36585000-36595000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:36585000-36598200	Strong transcription	Thymus	Thymus
39	chr19:36585000-36601600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr19:36585000-36602400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:36585200-36593400	Weak transcription	GM12878-XiMat	blood
42	chr19:36585200-36593600	Weak transcription	Hela-S3	cervix
43	chr19:36585200-36594800	Weak transcription	Osteobl	bone
44	chr19:36585200-36604400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr19:36586600-36594800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:36587000-36594400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:36587400-36598600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr19:36587600-36598800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:36588200-36598600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:36588400-36594800	Weak transcription	Stomach Smooth Muscle	stomach

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