Variant report

Variant	rs212714
Chromosome Location	chr2:32460348-32460349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32456174..32459090-chr2:32459159..32461418,3	MCF-7	breast:
2	chr2:32459736..32462357-chr2:32463296..32464848,2	K562	blood:
3	chr2:32458865..32461790-chr2:32581135..32583548,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115760	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11124274	0.89[GIH][hapmap]
rs11676938	0.91[GIH][hapmap];0.81[YRI][hapmap]
rs11678119	0.93[GIH][hapmap]
rs12614686	0.93[GIH][hapmap]
rs12989936	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs13017189	0.87[GIH][hapmap];0.85[TSI][hapmap]
rs13022197	0.91[GIH][hapmap]
rs177083	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.81[ASN][1000 genomes]
rs212695	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs212698	0.87[AMR][1000 genomes]
rs212699	0.80[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212700	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs212701	0.80[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212704	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs212706	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs212707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs212708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[ASN][1000 genomes]
rs212713	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[ASN][1000 genomes]
rs212715	0.83[CEU][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs212716	0.93[GIH][hapmap];0.81[LWK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs212717	0.83[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs212718	0.83[EUR][1000 genomes]
rs212721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212722	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212723	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212724	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212725	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212726	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212727	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212728	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212730	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212731	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212732	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs212733	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212735	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212737	0.87[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212739	0.80[EUR][1000 genomes]
rs212745	0.81[YRI][hapmap]
rs212758	0.87[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs212759	0.87[ASW][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.80[AMR][1000 genomes]
rs2280967	0.91[GIH][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs2365555	0.87[TSI][hapmap]
rs2566483	0.81[EUR][1000 genomes]
rs3769602	0.91[GIH][hapmap]
rs3769604	0.93[GIH][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap]
rs3769606	0.91[GIH][hapmap]
rs408813	0.81[EUR][1000 genomes]
rs430759	0.80[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs435572	0.85[GIH][hapmap];0.85[TSI][hapmap]
rs443609	0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs455060	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494569	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57903075	0.97[ASN][1000 genomes]
rs59966205	0.81[EUR][1000 genomes]
rs659239	0.85[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6723154	0.93[GIH][hapmap]
rs6725184	0.91[GIH][hapmap]
rs6737500	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs6760105	0.91[GIH][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap]
rs7561519	0.91[GIH][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs7577696	0.85[GIH][hapmap];0.83[TSI][hapmap]
rs7581340	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs7601267	0.85[GIH][hapmap];0.81[TSI][hapmap]
rs7605242	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers 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	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv2667	chr2:32444810-32489755	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs212714	SLC30A6	cis	cerebellum	SCAN
rs212714	EHD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32404200-32460600	Weak transcription	Esophagus	oesophagus
2	chr2:32443000-32483600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:32443200-32483800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:32445800-32461400	Weak transcription	Psoas Muscle	Psoas
5	chr2:32447400-32483800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:32448200-32460800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:32448200-32462400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:32448400-32474800	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:32448600-32460800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:32448800-32465400	Weak transcription	Osteobl	bone
11	chr2:32448800-32467000	Weak transcription	Left Ventricle	heart
12	chr2:32448800-32475600	Weak transcription	Lung	lung
13	chr2:32448800-32484800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:32449000-32463200	Weak transcription	HSMMtube	muscle
15	chr2:32451400-32462800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:32451400-32463200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:32451400-32466400	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:32451600-32460600	Weak transcription	Brain Anterior Caudate	brain
19	chr2:32451600-32461200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:32451600-32461400	Weak transcription	Fetal Intestine Large	intestine
21	chr2:32451600-32461400	Weak transcription	Fetal Stomach	stomach
22	chr2:32451600-32462000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:32451600-32463200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:32451600-32464000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:32451600-32464000	Weak transcription	NH-A	brain
26	chr2:32451600-32464800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:32451600-32466200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:32451600-32466400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:32451600-32475600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:32451800-32467600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:32452000-32475400	Weak transcription	Spleen	Spleen
32	chr2:32452200-32463200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:32452200-32466400	Weak transcription	Liver	Liver
34	chr2:32452200-32467400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:32452200-32468200	Weak transcription	Primary T cells from cord blood	blood
36	chr2:32452200-32479400	Weak transcription	Adipose Nuclei	Adipose
37	chr2:32452600-32461600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:32452600-32467200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:32457400-32465000	Weak transcription	A549	lung
40	chr2:32458200-32462200	Weak transcription	Primary B cells from cord blood	blood
41	chr2:32458800-32461200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:32459000-32461200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:32459400-32461200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:32459400-32461400	Enhancers	HMEC	breast
45	chr2:32459800-32460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:32459800-32461400	Enhancers	NHEK	skin
47	chr2:32460000-32460400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:32460000-32461200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:32460000-32462200	Strong transcription	HSMM	muscle
50	chr2:32460000-32477000	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links