Variant report

Variant	rs2246704
Chromosome Location	chr22:32349063-32349064
allele	C/T
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	NFIC	chr22:32348330-32349071	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr22:32348475-32349150	MCF10A-Er-Src	breast:	n/a	n/a
3	TCF12	chr22:32348324-32349077	SK-N-SH	brain:	n/a	n/a
4	STAT3	chr22:32348411-32349222	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr22:32348808-32349186	HepG2	liver:	n/a	n/a
6	POLR2A	chr22:32348028-32349183	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr22:32348434-32349208	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr22:32348445-32349367	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr22:32339799-32349498	K562	blood:	n/a	n/a
10	FOS	chr22:32348445-32349078	MCF10A-Er-Src	breast:	n/a	chr22:32348634-32348645 chr22:32348608-32348618
11	STAT3	chr22:32348471-32349273	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr22:32348422-32349280	MCF10A-Er-Src	breast:	n/a	chr22:32348634-32348645 chr22:32348608-32348618
13	FOS	chr22:32348212-32349153	MCF10A-Er-Src	breast:	n/a	chr22:32348634-32348645 chr22:32348608-32348618

No.	Distal block	Cell Line	Cell type
1	22:32053085-32061138..22:32347255-32351014	GM12878	blood:
2	22:32170492-32188129..22:32347255-32351014	K562	blood:
3	22:32012966-32043914..22:32347255-32351014	K562	blood:
4	22:31864703-31891033..22:32347255-32351014	K562	blood:
5	chr22:32346636..32349380-chr22:32349950..32352854,3	K562	blood:

Variant related genes	Relation type
ENSG00000238910	TF binding region
ENSG00000198089	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000199248	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000100150	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1049583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12168840	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs130262	0.92[CEU][hapmap]
rs130266	0.81[CEU][hapmap]
rs13055495	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs135021	0.92[CEU][hapmap]
rs135023	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs135110	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs135111	0.80[CEU][hapmap]
rs16989702	0.93[YRI][hapmap]
rs1807550	0.85[EUR][1000 genomes]
rs1986211	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2301415	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs2413061	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2853884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2853887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2858750	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs2858752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2858753	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3747158	0.84[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs4820059	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820065	0.82[EUR][1000 genomes]
rs4821004	0.92[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5753852	0.90[CEU][hapmap]
rs5994457	0.85[EUR][1000 genomes]
rs5994458	0.80[EUR][1000 genomes]
rs5994461	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5998196	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5998198	0.82[EUR][1000 genomes]
rs5998201	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5998204	0.84[EUR][1000 genomes]
rs5998233	0.81[CEU][hapmap]
rs5998237	0.81[CEU][hapmap]
rs7290696	0.88[CHB][hapmap]
rs7291050	0.88[CHB][hapmap]
rs7364274	0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs738181	0.88[CHB][hapmap]
rs8137665	0.81[CEU][hapmap]
rs8141011	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs8142505	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs93108	0.92[CEU][hapmap]
rs933226	0.88[CHB][hapmap]
rs9606906	0.81[CEU][hapmap]
rs9609394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9609395	0.91[ASN][1000 genomes]
rs9621371	0.88[CHB][hapmap];0.86[CHD][hapmap]

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	nsv428046	chr22:32316302-32356963	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2246704	CHEK2	cis	cerebellum	SCAN
rs2246704	LARGE	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32342000-32354400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:32342400-32357600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:32343400-32350400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr22:32343400-32355000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:32343600-32349200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr22:32343600-32349800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
7	chr22:32343600-32354600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:32343800-32351000	Strong transcription	Primary B cells from cord blood	blood
9	chr22:32344600-32352200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:32344800-32352000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr22:32345600-32349200	Genic enhancers	NHDF-Ad	bronchial
12	chr22:32345600-32350000	Enhancers	Fetal Brain Male	brain
13	chr22:32345600-32350800	Genic enhancers	HMEC	breast
14	chr22:32345600-32351200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr22:32345600-32351200	Genic enhancers	Fetal Brain Female	brain
16	chr22:32345800-32350000	Enhancers	Hela-S3	cervix
17	chr22:32345800-32351000	Genic enhancers	NHEK	skin
18	chr22:32345800-32351400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr22:32345800-32352600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr22:32346200-32349400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr22:32346200-32349400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr22:32346200-32350800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr22:32346200-32350800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr22:32346400-32350600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr22:32346400-32351200	Genic enhancers	Rectal Mucosa Donor 31	rectum
26	chr22:32346600-32351000	Enhancers	Colon Smooth Muscle	Colon
27	chr22:32346600-32351200	Enhancers	Brain Anterior Caudate	brain
28	chr22:32346600-32351600	Enhancers	HUVEC	blood vessel
29	chr22:32346600-32352200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr22:32346600-32352800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr22:32346600-32356400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr22:32346800-32350200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr22:32346800-32351200	Enhancers	Adipose Nuclei	Adipose
34	chr22:32346800-32351200	Enhancers	Stomach Mucosa	stomach
35	chr22:32346800-32351400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr22:32346800-32351400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr22:32346800-32352200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr22:32346800-32354800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:32347000-32350600	Weak transcription	Fetal Intestine Small	intestine
40	chr22:32347000-32351000	Weak transcription	Fetal Lung	lung
41	chr22:32347000-32351200	Enhancers	Thymus	Thymus
42	chr22:32347200-32349200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
43	chr22:32347200-32349600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
44	chr22:32347200-32350200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr22:32347200-32350200	Enhancers	NH-A	brain
46	chr22:32347200-32350600	Weak transcription	Lung	lung
47	chr22:32347200-32350800	Enhancers	Small Intestine	intestine
48	chr22:32347200-32351200	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr22:32347200-32351200	Enhancers	Rectal Smooth Muscle	rectum
50	chr22:32347200-32355000	Strong transcription	Fetal Muscle Trunk	muscle

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