Variant report

Variant	rs212713
Chromosome Location	chr2:32457537-32457538
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:32456174..32459090-chr2:32459159..32461418,3	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10172468	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs10208246	0.92[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs11124278	0.89[EUR][1000 genomes]
rs11676475	0.81[EUR][1000 genomes]
rs12465351	1.00[CEU][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs12474598	0.81[EUR][1000 genomes]
rs12997026	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13017189	0.82[GIH][hapmap]
rs13427170	0.92[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs177083	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212686	0.92[EUR][1000 genomes]
rs212687	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.92[EUR][1000 genomes]
rs212694	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs212699	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs212700	0.86[ASN][1000 genomes]
rs212701	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs212703	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs212704	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs212705	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs212706	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs212707	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs212708	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs212714	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[ASN][1000 genomes]
rs212721	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs212722	0.92[ASN][1000 genomes]
rs212723	0.92[ASN][1000 genomes]
rs212724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs212725	0.91[ASN][1000 genomes]
rs212726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs212727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[ASN][1000 genomes]
rs212728	0.92[ASN][1000 genomes]
rs212730	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs212731	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[ASN][1000 genomes]
rs212732	0.86[ASN][1000 genomes]
rs212733	0.92[ASN][1000 genomes]
rs212734	0.92[ASN][1000 genomes]
rs212735	0.92[ASN][1000 genomes]
rs212737	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs212738	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs212740	0.82[EUR][1000 genomes]
rs212741	0.85[EUR][1000 genomes]
rs212743	0.87[EUR][1000 genomes]
rs212744	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs212748	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs212749	0.85[EUR][1000 genomes]
rs212752	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs212753	0.91[EUR][1000 genomes]
rs212755	1.00[CEU][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs212756	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs212757	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs212758	0.89[CHD][hapmap];0.91[JPT][hapmap]
rs212759	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs212762	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs216544	0.83[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs2366736	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs430759	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4407291	0.86[EUR][1000 genomes]
rs4519572	0.86[EUR][1000 genomes]
rs455060	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs467523	0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs494569	0.88[ASN][1000 genomes]
rs4952209	1.00[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4952252	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs55877106	0.83[EUR][1000 genomes]
rs57903075	0.91[ASN][1000 genomes]
rs62134021	0.83[EUR][1000 genomes]
rs6716179	1.00[CEU][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs6717209	1.00[CEU][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs7577696	0.84[GIH][hapmap]
rs7581432	1.00[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7588883	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs7601267	0.84[GIH][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
rs212713	NLRC4	cis	lymphoblastoid	seeQTL
rs212713	EHD3	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

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	chr2:32448200-32458400	Weak transcription	NHDF-Ad	bronchial
7	chr2:32448200-32460800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:32448200-32462400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:32448400-32474800	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:32448600-32460800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:32448800-32457800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:32448800-32459000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:32448800-32465400	Weak transcription	Osteobl	bone
14	chr2:32448800-32467000	Weak transcription	Left Ventricle	heart
15	chr2:32448800-32475600	Weak transcription	Lung	lung
16	chr2:32448800-32484800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:32449000-32459000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:32449000-32463200	Weak transcription	HSMMtube	muscle
19	chr2:32450600-32459400	Weak transcription	NHEK	skin
20	chr2:32451400-32462800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:32451400-32463200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr2:32451400-32466400	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:32451600-32457600	Weak transcription	Ovary	ovary
24	chr2:32451600-32458400	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:32451600-32459400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:32451600-32459600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:32451600-32459600	Weak transcription	Aorta	Aorta
28	chr2:32451600-32459600	Weak transcription	HSMM	muscle
29	chr2:32451600-32459800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:32451600-32459800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:32451600-32460000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:32451600-32460600	Weak transcription	Brain Anterior Caudate	brain
33	chr2:32451600-32461200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:32451600-32461400	Weak transcription	Fetal Intestine Large	intestine
35	chr2:32451600-32461400	Weak transcription	Fetal Stomach	stomach
36	chr2:32451600-32462000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:32451600-32463200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:32451600-32464000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:32451600-32464000	Weak transcription	NH-A	brain
40	chr2:32451600-32464800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:32451600-32466200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:32451600-32466400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:32451600-32475600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:32451800-32467600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:32452000-32475400	Weak transcription	Spleen	Spleen
46	chr2:32452200-32463200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:32452200-32466400	Weak transcription	Liver	Liver
48	chr2:32452200-32467400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:32452200-32468200	Weak transcription	Primary T cells from cord blood	blood
50	chr2:32452200-32479400	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links