Variant report

Variant	rs4907237
Chromosome Location	chr2:97190497-97190498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:97186999..97193890-chr2:97195304..97199298,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235480	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10460601	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11164095	0.82[EUR][1000 genomes]
rs11164109	0.81[EUR][1000 genomes]
rs1122238	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678174	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11682934	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11691670	0.83[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12469420	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2118836	0.82[EUR][1000 genomes]
rs2278563	0.87[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3731935	0.85[MKK][hapmap]
rs4907236	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4907238	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907240	0.83[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4907241	0.83[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4907242	0.90[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs62154845	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6747149	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6749159	0.83[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6759099	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7575254	0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4907237	KIAA1310	cis	multi-tissue	Pritchard
rs4907237	CIAO1	cis	lymphoblastoid	seeQTL
rs4907237	MGAT4A	cis	parietal	SCAN
rs4907237	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97174400-97193000	Weak transcription	Right Atrium	heart
2	chr2:97187600-97192200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr2:97187800-97190800	Enhancers	Placenta	Placenta
4	chr2:97188600-97190600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr2:97188600-97190800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:97188600-97191000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:97188800-97190800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:97189200-97191000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:97189400-97190600	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr2:97189400-97191000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:97189400-97191200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:97189400-97191200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:97189600-97190600	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr2:97189600-97190600	Flanking Active TSS	GM12878-XiMat	blood
15	chr2:97189600-97190800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:97189600-97191000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:97189600-97191000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:97189600-97191200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr2:97189600-97192400	Weak transcription	Right Ventricle	heart
20	chr2:97189800-97191000	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:97189800-97192800	Weak transcription	Lung	lung
22	chr2:97189800-97193000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:97190000-97190600	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:97190000-97191000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:97190000-97191600	Weak transcription	Fetal Thymus	thymus
26	chr2:97190000-97192400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:97190000-97192600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:97190200-97190600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:97190200-97191000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:97190200-97192800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:97190200-97192800	Weak transcription	Adipose Nuclei	Adipose
32	chr2:97190200-97192800	Enhancers	NHDF-Ad	bronchial
33	chr2:97190400-97190600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:97190400-97190600	Enhancers	Spleen	Spleen
35	chr2:97190400-97191200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:97190400-97191200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:97190400-97191400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:97190400-97192000	Enhancers	Esophagus	oesophagus

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