Variant report

Variant	rs212679
Chromosome Location	chr2:32431107-32431108
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:32389554..32392217-chr2:32429734..32432674,3	K562	blood:

Variant related genes	Relation type
ENSG00000152683	Chromatin interaction
ENSG00000272716	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10172468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10208246	0.95[JPT][hapmap]
rs10490360	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs11124274	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs11124275	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs11124276	0.89[EUR][1000 genomes]
rs11124277	0.89[EUR][1000 genomes]
rs11676938	0.89[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs11678119	0.81[JPT][hapmap];0.85[YRI][hapmap]
rs11681731	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11686061	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12465351	0.91[JPT][hapmap];0.80[YRI][hapmap]
rs12474443	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12614686	0.91[JPT][hapmap]
rs12617289	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12617290	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12620922	0.82[EUR][1000 genomes]
rs1265340	0.81[EUR][1000 genomes]
rs1265341	0.86[EUR][1000 genomes]
rs12989936	0.89[CEU][hapmap]
rs12997026	0.91[JPT][hapmap]
rs13000753	0.81[EUR][1000 genomes]
rs13017189	0.95[CEU][hapmap]
rs13022197	0.95[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13024004	0.81[EUR][1000 genomes]
rs13029752	0.81[EUR][1000 genomes]
rs13427170	0.91[JPT][hapmap]
rs17767988	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs212678	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs212680	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs212686	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs212687	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs212695	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs212698	0.89[EUR][1000 genomes]
rs212699	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs212700	0.85[EUR][1000 genomes]
rs212701	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs212703	0.82[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs212715	0.90[CEU][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs212716	0.84[CEU][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs212717	0.89[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs212718	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs212722	0.85[EUR][1000 genomes]
rs212723	0.87[EUR][1000 genomes]
rs212724	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs212725	0.89[EUR][1000 genomes]
rs212726	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs212727	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs212728	0.89[EUR][1000 genomes]
rs212730	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs212731	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs212733	0.86[EUR][1000 genomes]
rs212735	0.89[EUR][1000 genomes]
rs212737	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs212738	0.91[JPT][hapmap]
rs212739	0.95[CEU][hapmap];0.96[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs212740	0.87[ASN][1000 genomes]
rs212741	0.87[ASN][1000 genomes]
rs212743	0.92[ASN][1000 genomes]
rs212744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs212745	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs212746	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs212748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs212749	0.92[ASN][1000 genomes]
rs212753	0.93[ASN][1000 genomes]
rs212755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs212758	0.95[CEU][hapmap]
rs212759	0.95[CEU][hapmap]
rs212760	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs216544	0.86[JPT][hapmap]
rs2235134	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2280967	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs2365555	0.95[CEU][hapmap]
rs2365558	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2366736	0.96[JPT][hapmap]
rs2566483	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34856365	0.83[EUR][1000 genomes]
rs36014814	0.82[EUR][1000 genomes]
rs374743	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3752916	0.96[JPT][hapmap]
rs3769602	0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs3769604	0.89[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs3769606	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs3851310	0.80[CEU][hapmap]
rs408813	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs428002	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs430759	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs435572	0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs443609	0.84[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs455060	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs466126	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs467523	0.82[JPT][hapmap]
rs469305	0.81[CEU][hapmap]
rs479333	0.84[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs494569	0.86[EUR][1000 genomes]
rs4952209	0.95[JPT][hapmap]
rs4952247	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4952248	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs4952249	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4952250	0.95[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4952252	0.95[JPT][hapmap]
rs55877106	0.99[ASN][1000 genomes]
rs56740303	0.83[EUR][1000 genomes]
rs59966205	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62134021	0.93[ASN][1000 genomes]
rs62134033	0.82[EUR][1000 genomes]
rs6543649	0.92[EUR][1000 genomes]
rs659239	0.84[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6716179	0.90[JPT][hapmap]
rs6717209	0.91[JPT][hapmap];0.81[YRI][hapmap]
rs6723154	0.91[JPT][hapmap]
rs6725184	0.95[CEU][hapmap]
rs6737500	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs6738349	0.86[EUR][1000 genomes]
rs6747488	0.88[EUR][1000 genomes]
rs6748621	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs6752375	0.86[JPT][hapmap]
rs6758024	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs6760105	0.95[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs7559964	0.89[EUR][1000 genomes]
rs7561519	0.89[CEU][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs7566162	0.90[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs7572964	0.91[JPT][hapmap]
rs7573543	0.95[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7575139	0.81[EUR][1000 genomes]
rs7577408	0.83[EUR][1000 genomes]
rs7577696	0.95[CEU][hapmap]
rs7581032	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7581340	0.85[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7581432	0.91[JPT][hapmap]
rs7586448	0.90[CEU][hapmap]
rs7588883	0.91[JPT][hapmap]
rs7601267	0.89[CEU][hapmap]
rs7605242	0.90[CEU][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes]
rs9677104	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs212679	NLRC4	cis	Lymphoblastoid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:32391800-32431400	Weak transcription	Stomach Mucosa	stomach
3	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
4	chr2:32392000-32435800	Weak transcription	NHLF	lung
5	chr2:32392200-32445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:32392800-32447600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:32399200-32449600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:32403000-32452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:32404200-32445200	Weak transcription	Brain Angular Gyrus	brain
10	chr2:32404200-32447600	Weak transcription	Pancreas	Pancrea
11	chr2:32404200-32448000	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:32404200-32452400	Weak transcription	Right Ventricle	heart
13	chr2:32404200-32460600	Weak transcription	Esophagus	oesophagus
14	chr2:32404400-32447400	Weak transcription	HUVEC	blood vessel
15	chr2:32404400-32450800	Weak transcription	Gastric	stomach
16	chr2:32404800-32434000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:32404800-32447800	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:32408000-32435800	Weak transcription	Psoas Muscle	Psoas
19	chr2:32410400-32436000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:32410400-32445200	Weak transcription	Fetal Kidney	kidney
21	chr2:32410600-32445200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:32411400-32445400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:32411600-32447800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:32412000-32450400	Weak transcription	Spleen	Spleen
25	chr2:32412200-32444200	Weak transcription	Fetal Brain Female	brain
26	chr2:32412800-32445200	Weak transcription	Brain Substantia Nigra	brain
27	chr2:32413200-32433600	Weak transcription	Fetal Lung	lung
28	chr2:32415200-32445200	Weak transcription	HMEC	breast
29	chr2:32415600-32432400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:32419200-32446800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:32419800-32434000	Weak transcription	NHDF-Ad	bronchial
32	chr2:32419800-32445200	Weak transcription	HSMM	muscle
33	chr2:32420200-32432400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:32420800-32447000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:32421000-32432200	Strong transcription	Adipose Nuclei	Adipose
36	chr2:32421200-32445000	Weak transcription	Thymus	Thymus
37	chr2:32421200-32445400	Weak transcription	Fetal Heart	heart
38	chr2:32421400-32443000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:32422000-32452400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:32423000-32443200	Weak transcription	GM12878-XiMat	blood
41	chr2:32423000-32447400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:32423400-32448000	Weak transcription	Small Intestine	intestine
43	chr2:32423600-32433800	Strong transcription	Fetal Stomach	stomach
44	chr2:32423600-32445200	Weak transcription	NH-A	brain
45	chr2:32424200-32435200	Weak transcription	Left Ventricle	heart
46	chr2:32424200-32436800	Weak transcription	Brain Germinal Matrix	brain
47	chr2:32424400-32433600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:32424400-32438400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:32424400-32445200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:32424400-32447400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links