Variant report

Variant	rs212708
Chromosome Location	chr2:32451446-32451447
allele	C/T
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	chr2:32451148..32452935-chr2:32453528..32455785,2	K562	blood:
3	chr2:32445227..32449129-chr2:32451328..32453997,4	K562	blood:
4	chr2:32435157..32437239-chr2:32449933..32452199,2	K562	blood:
5	chr2:32390601..32392270-chr2:32450948..32453894,2	MCF-7	breast:
6	chr2:32450716..32453123-chr2:32453250..32456033,3	MCF-7	breast:
7	chr2:32451081..32452778-chr2:32461639..32463751,2	K562	blood:

Variant related genes	Relation type
ENSG00000152683	Chromatin interaction
ENSG00000272716	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12465351	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs12997026	0.83[CEU][hapmap]
rs177083	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212687	0.83[CEU][hapmap];0.81[LWK][hapmap];0.86[YRI][hapmap]
rs212694	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs212695	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs212698	0.84[ASN][1000 genomes]
rs212699	1.00[CHB][hapmap];0.98[CHD][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];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs212703	0.83[CEU][hapmap];0.86[YRI][hapmap]
rs212704	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]
rs212705	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs212706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212713	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];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][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];0.85[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[ASN][1000 genomes]
rs212731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][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];0.82[ASN][1000 genomes]
rs212738	0.83[CEU][hapmap]
rs212744	0.83[CEU][hapmap]
rs212748	0.83[CEU][hapmap]
rs212752	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs212755	0.83[CEU][hapmap]
rs212756	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs212757	0.84[AFR][1000 genomes];0.90[AMR][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]
rs2366736	0.83[CEU][hapmap]
rs430759	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs455060	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4952209	0.83[CEU][hapmap]
rs4952252	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs57903075	0.81[ASN][1000 genomes]
rs6716179	0.83[CEU][hapmap]
rs6717209	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs7581432	0.83[CEU][hapmap];0.80[MEX][hapmap]
rs7588883	0.83[CEU][hapmap];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs212708	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 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	chr2:32422000-32452400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:32424400-32455400	Weak transcription	Fetal Brain Male	brain
8	chr2:32426400-32455000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:32433800-32451600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:32435200-32451600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:32438800-32452400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:32442800-32452200	Strong transcription	Liver	Liver
13	chr2:32443000-32451600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:32443000-32483600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:32443200-32451600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:32443200-32483800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:32444400-32451600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:32444600-32452200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:32444800-32451600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:32444800-32451800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:32444800-32452600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:32444800-32452800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:32445200-32452600	Strong transcription	Placenta	Placenta
24	chr2:32445800-32452200	Weak transcription	Fetal Heart	heart
25	chr2:32445800-32452400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:32445800-32461400	Weak transcription	Psoas Muscle	Psoas
27	chr2:32446200-32456400	Weak transcription	NHLF	lung
28	chr2:32447200-32451600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:32447200-32451600	Strong transcription	Fetal Thymus	thymus
30	chr2:32447200-32452200	Strong transcription	Primary T cells from cord blood	blood
31	chr2:32447200-32452200	Strong transcription	Adipose Nuclei	Adipose
32	chr2:32447400-32451600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:32447400-32451600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:32447400-32451600	Strong transcription	Fetal Muscle Leg	muscle
35	chr2:32447400-32451600	Strong transcription	HSMM	muscle
36	chr2:32447400-32452600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:32447400-32483800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:32447600-32451600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:32447600-32452600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:32448200-32452800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:32448200-32452800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:32448200-32453000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:32448200-32458400	Weak transcription	NHDF-Ad	bronchial
44	chr2:32448200-32460800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:32448200-32462400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:32448400-32453000	Weak transcription	Dnd41	blood
47	chr2:32448400-32453600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:32448400-32474800	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:32448600-32452600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:32448600-32460800	Weak transcription	Brain Inferior Temporal Lobe	brain

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