Variant report

Variant	rs7720243
Chromosome Location	chr5:112715238-112715239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112714749..112715324-chr5:112848849..112849777,2	K562	blood:
2	chr5:112714356..112715276-chr5:112847595..112848868,4	MCF-7	breast:
3	chr5:112714624..112715315-chr5:112847050..112847731,2	MCF-7	breast:
4	chr5:112714439..112715552-chr5:112846186..112846977,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10037845	0.87[YRI][hapmap]
rs10042401	1.00[ASW][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap]
rs10043512	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10050553	1.00[ASW][hapmap];0.88[MKK][hapmap]
rs10054914	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10055294	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10061063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10070884	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10077495	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10078931	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10478122	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11951897	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11960242	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12110055	0.85[YRI][hapmap]
rs13358281	0.87[YRI][hapmap]
rs7719254	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7720243	CHI3L2	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112700800-112718000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:112707800-112719000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:112708000-112716200	Weak transcription	Fetal Kidney	kidney
4	chr5:112711400-112716200	Weak transcription	NH-A	brain
5	chr5:112711800-112716200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:112712600-112715400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:112712600-112715800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:112713000-112715400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:112714000-112717000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:112714200-112715600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:112714200-112717000	Enhancers	Fetal Stomach	stomach
12	chr5:112714400-112715600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:112714400-112716200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr5:112714400-112717200	Enhancers	Fetal Heart	heart
15	chr5:112714600-112716400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr5:112714600-112717000	Enhancers	Fetal Lung	lung
17	chr5:112714800-112715600	Enhancers	Primary T cells from cord blood	blood
18	chr5:112714800-112718600	Enhancers	Dnd41	blood
19	chr5:112715000-112715400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:112715000-112716200	Enhancers	Rectal Smooth Muscle	rectum
21	chr5:112715000-112716400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:112715000-112720600	Weak transcription	Aorta	Aorta
23	chr5:112715200-112715600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr5:112715200-112716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:112715200-112716200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:112715200-112716200	Weak transcription	HMEC	breast
27	chr5:112715200-112716800	Weak transcription	NHEK	skin
28	chr5:112715200-112718200	Weak transcription	HUVEC	blood vessel

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