Variant report

Variant	rs212704
Chromosome Location	chr2:32450348-32450349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32449383..32452935-chr2:32453353..32456316,4	K562	blood:
2	chr2:32449383..32451061-chr2:32453847..32456316,2	K562	blood:
3	chr2:32435157..32437239-chr2:32449933..32452199,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10172468	0.81[EUR][1000 genomes]
rs10208246	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs11124278	0.86[EUR][1000 genomes]
rs12465351	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs12997026	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs13427170	0.88[CEU][hapmap];0.91[GIH][hapmap]
rs177083	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212686	0.89[EUR][1000 genomes]
rs212687	0.96[CEU][hapmap];0.91[GIH][hapmap];0.89[EUR][1000 genomes]
rs212694	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs212695	0.83[ASN][1000 genomes]
rs212698	0.84[ASN][1000 genomes]
rs212699	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs212700	0.96[ASN][1000 genomes]
rs212701	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs212703	0.96[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs212705	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs212706	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212707	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212708	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212713	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]
rs212714	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs212721	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs212722	0.82[ASN][1000 genomes]
rs212723	0.82[ASN][1000 genomes]
rs212724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs212725	0.81[ASN][1000 genomes]
rs212726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs212727	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[ASN][1000 genomes]
rs212728	0.82[ASN][1000 genomes]
rs212730	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[ASN][1000 genomes]
rs212731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs212733	0.82[ASN][1000 genomes]
rs212734	0.82[ASN][1000 genomes]
rs212735	0.82[ASN][1000 genomes]
rs212737	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.82[ASN][1000 genomes]
rs212738	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs212741	0.83[EUR][1000 genomes]
rs212743	0.84[EUR][1000 genomes]
rs212744	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs212748	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs212749	0.82[EUR][1000 genomes]
rs212752	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs212753	0.88[EUR][1000 genomes]
rs212755	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs212756	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212757	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212758	0.87[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs212759	0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs212762	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs216544	0.88[GIH][hapmap]
rs2366736	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs430759	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.97[ASN][1000 genomes]
rs4407291	0.83[EUR][1000 genomes]
rs4519572	0.84[EUR][1000 genomes]
rs455060	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[ASN][1000 genomes]
rs467523	0.84[CEU][hapmap];0.91[GIH][hapmap]
rs4952209	0.96[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs4952252	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs55877106	0.81[EUR][1000 genomes]
rs57903075	0.81[ASN][1000 genomes]
rs62134021	0.80[EUR][1000 genomes]
rs6716179	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6717209	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7581432	0.96[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs7588883	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]

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
rs212704	NLRC4	cis	lymphoblastoid	seeQTL
rs212704	EHD3	cis	parietal	SCAN

Chromatin state (count:116 , 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	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
3	chr2:32403000-32452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:32404200-32452400	Weak transcription	Right Ventricle	heart
5	chr2:32404200-32460600	Weak transcription	Esophagus	oesophagus
6	chr2:32404400-32450800	Weak transcription	Gastric	stomach
7	chr2:32412000-32450400	Weak transcription	Spleen	Spleen
8	chr2:32422000-32452400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:32424400-32455400	Weak transcription	Fetal Brain Male	brain
10	chr2:32426400-32455000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:32433800-32451600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:32435200-32451600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:32438800-32452400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:32442800-32452200	Strong transcription	Liver	Liver
15	chr2:32443000-32451600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:32443000-32483600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:32443200-32451600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:32443200-32483800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:32444400-32451600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:32444600-32451400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:32444600-32451400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:32444600-32452200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:32444800-32451600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:32444800-32451800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:32444800-32452600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:32444800-32452800	Weak transcription	Fetal Intestine Small	intestine
27	chr2:32445200-32452600	Strong transcription	Placenta	Placenta
28	chr2:32445800-32451000	Weak transcription	Fetal Stomach	stomach
29	chr2:32445800-32452200	Weak transcription	Fetal Heart	heart
30	chr2:32445800-32452400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:32445800-32461400	Weak transcription	Psoas Muscle	Psoas
32	chr2:32446000-32450600	Weak transcription	Hela-S3	cervix
33	chr2:32446200-32456400	Weak transcription	NHLF	lung
34	chr2:32447200-32451400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:32447200-32451600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:32447200-32451600	Strong transcription	Fetal Thymus	thymus
37	chr2:32447200-32452200	Strong transcription	Primary T cells from cord blood	blood
38	chr2:32447200-32452200	Strong transcription	Adipose Nuclei	Adipose
39	chr2:32447400-32451600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:32447400-32451600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:32447400-32451600	Strong transcription	Fetal Muscle Leg	muscle
42	chr2:32447400-32451600	Strong transcription	HSMM	muscle
43	chr2:32447400-32452600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:32447400-32483800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:32447600-32451200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:32447600-32451600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:32447600-32452600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:32447800-32451400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:32448200-32450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:32448200-32450800	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links