Variant report

Variant	rs212746
Chromosome Location	chr2:32413067-32413068
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	chr2:32389125..32392352-chr2:32409870..32414228,3	K562	blood:

Variant related genes	Relation type
ENSG00000152683	Chromatin interaction
ENSG00000272716	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10172468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10208246	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10490360	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11124274	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs11124275	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11124276	0.90[EUR][1000 genomes]
rs11124277	0.90[EUR][1000 genomes]
rs11124278	0.82[ASN][1000 genomes]
rs11676938	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs11678119	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs11681731	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11683760	0.90[AFR][1000 genomes]
rs11683842	0.83[AFR][1000 genomes]
rs11683931	0.80[EUR][1000 genomes]
rs11686061	0.90[EUR][1000 genomes]
rs11689817	0.85[AFR][1000 genomes]
rs11694630	0.91[AFR][1000 genomes]
rs12465351	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12474443	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12611678	0.87[AFR][1000 genomes]
rs12614686	0.84[CEU][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes]
rs12617289	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12617290	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12618002	0.87[AFR][1000 genomes]
rs12620922	0.83[EUR][1000 genomes]
rs1265341	0.83[EUR][1000 genomes]
rs12989936	0.95[CEU][hapmap]
rs12995952	0.91[AFR][1000 genomes]
rs12997026	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs13000753	0.82[EUR][1000 genomes]
rs13007972	0.87[AFR][1000 genomes]
rs13008192	0.80[AFR][1000 genomes]
rs13017189	1.00[CEU][hapmap]
rs13022197	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13024004	0.82[EUR][1000 genomes]
rs13029752	0.82[EUR][1000 genomes]
rs13427170	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17767988	1.00[CEU][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs212678	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212679	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]
rs212686	0.92[ASN][1000 genomes]
rs212687	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs212695	0.91[EUR][1000 genomes]
rs212698	0.86[EUR][1000 genomes]
rs212699	0.94[CEU][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs212700	0.82[EUR][1000 genomes]
rs212701	0.94[CEU][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs212703	0.82[JPT][hapmap]
rs212715	0.95[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs212716	0.89[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs212717	0.94[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs212718	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs212722	0.82[EUR][1000 genomes]
rs212723	0.84[EUR][1000 genomes]
rs212724	0.95[CEU][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes]
rs212725	0.86[EUR][1000 genomes]
rs212726	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs212727	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs212728	0.86[EUR][1000 genomes]
rs212730	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs212731	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs212733	0.83[EUR][1000 genomes]
rs212735	0.86[EUR][1000 genomes]
rs212737	0.89[CEU][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs212738	0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs212739	1.00[CEU][hapmap];0.96[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs212740	0.93[ASN][1000 genomes]
rs212741	0.94[ASN][1000 genomes]
rs212743	0.99[ASN][1000 genomes]
rs212744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs212745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs212749	0.95[ASN][1000 genomes]
rs212753	0.96[ASN][1000 genomes]
rs212755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs212758	1.00[CEU][hapmap]
rs212759	1.00[CEU][hapmap]
rs212760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs212762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs216544	0.86[JPT][hapmap]
rs2235134	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2280967	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2294176	0.86[AFR][1000 genomes]
rs2294179	0.82[AFR][1000 genomes]
rs2365555	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs2365558	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2366736	0.96[JPT][hapmap]
rs2566483	0.89[EUR][1000 genomes]
rs34856365	0.84[EUR][1000 genomes]
rs34976640	0.81[AFR][1000 genomes]
rs36014814	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs374743	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3752916	0.80[CEU][hapmap];0.96[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3769602	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs3769604	0.95[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs3769606	0.95[CEU][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs3851310	0.84[CEU][hapmap]
rs408813	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4258846	0.81[ASN][1000 genomes]
rs428002	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs430759	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs435572	0.84[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4407291	0.81[ASN][1000 genomes]
rs443609	0.89[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs4519572	0.81[ASN][1000 genomes]
rs455060	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs466126	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs467523	0.82[JPT][hapmap]
rs469305	0.86[CEU][hapmap]
rs479333	0.89[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs494569	0.83[EUR][1000 genomes]
rs4952209	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4952247	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4952248	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs4952249	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4952250	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4952252	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs55877106	0.92[ASN][1000 genomes]
rs56740303	0.84[EUR][1000 genomes]
rs59966205	0.89[EUR][1000 genomes]
rs62134021	0.96[ASN][1000 genomes]
rs6543649	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs659239	0.89[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6716179	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6717209	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6723154	0.84[CEU][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes]
rs6725184	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6737500	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs6738349	0.87[EUR][1000 genomes]
rs6747488	0.89[EUR][1000 genomes]
rs6748621	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs6752375	0.86[JPT][hapmap]
rs6758024	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6760105	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs7559964	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7561519	0.95[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs7566162	0.95[CEU][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs7572964	0.80[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7573543	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7575139	0.82[EUR][1000 genomes]
rs7577408	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7577696	1.00[CEU][hapmap]
rs7581032	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7581340	0.90[CEU][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7581432	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7586448	0.95[CEU][hapmap]
rs7588883	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7592239	0.88[AFR][1000 genomes]
rs7592356	0.86[AFR][1000 genomes]
rs7601267	0.95[CEU][hapmap]
rs7604289	0.85[AFR][1000 genomes]
rs7605242	0.95[CEU][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs7608127	0.80[EUR][1000 genomes]
rs9677104	0.82[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
rs212746	NLRC4	cis	Lymphoblastoid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391600-32426400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:32391800-32431400	Weak transcription	Stomach Mucosa	stomach
4	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
5	chr2:32392000-32414600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:32392000-32435800	Weak transcription	NHLF	lung
7	chr2:32392200-32422800	Weak transcription	Fetal Brain Male	brain
8	chr2:32392200-32445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:32392800-32447600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:32396000-32414000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:32396200-32413600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:32399200-32449600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:32400800-32418800	Weak transcription	NHDF-Ad	bronchial
14	chr2:32403000-32452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:32403800-32426200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:32404200-32413800	Weak transcription	GM12878-XiMat	blood
17	chr2:32404200-32417600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:32404200-32445200	Weak transcription	Brain Angular Gyrus	brain
19	chr2:32404200-32447600	Weak transcription	Pancreas	Pancrea
20	chr2:32404200-32448000	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:32404200-32452400	Weak transcription	Right Ventricle	heart
22	chr2:32404200-32460600	Weak transcription	Esophagus	oesophagus
23	chr2:32404400-32414200	Weak transcription	HMEC	breast
24	chr2:32404400-32416800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:32404400-32423800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:32404400-32427800	Weak transcription	Aorta	Aorta
27	chr2:32404400-32447400	Weak transcription	HUVEC	blood vessel
28	chr2:32404400-32450800	Weak transcription	Gastric	stomach
29	chr2:32404800-32417600	Weak transcription	HSMM	muscle
30	chr2:32404800-32434000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:32404800-32447800	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:32405200-32418200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:32405400-32413800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:32405800-32414200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:32405800-32420600	Weak transcription	Left Ventricle	heart
36	chr2:32405800-32423800	Weak transcription	Ovary	ovary
37	chr2:32407000-32413200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:32407000-32413600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:32407200-32421600	Weak transcription	Small Intestine	intestine
40	chr2:32407400-32413400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:32407400-32413600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:32407400-32414400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:32407600-32413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:32408000-32418400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:32408000-32424000	Weak transcription	Brain Anterior Caudate	brain
46	chr2:32408000-32426000	Weak transcription	HSMMtube	muscle
47	chr2:32408000-32428000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:32408000-32435800	Weak transcription	Psoas Muscle	Psoas
49	chr2:32408400-32423800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:32408800-32414200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links