Variant report

Variant	rs10439444
Chromosome Location	chr2:32183767-32183768
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	chr2:32182331..32185618-chr2:32188893..32193404,4	K562	blood:
2	chr2:32182812..32184374-chr2:32389224..32392074,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272716	Chromatin interaction
ENSG00000152683	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10490360	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11124274	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11124275	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11676938	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs11678119	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs12614686	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap]
rs1272585	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs12989936	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs13000753	0.80[ASN][1000 genomes]
rs13017189	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs13022197	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs13024004	0.80[ASN][1000 genomes]
rs160797	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs160801	0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap]
rs17767988	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1904489	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1986134	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs216544	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap]
rs223621	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap]
rs223665	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap]
rs2280967	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2365555	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2366297	0.82[CHB][hapmap];0.89[YRI][hapmap]
rs3752916	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3769602	0.90[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs3769604	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs3769606	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs41280625	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs467523	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap]
rs4952248	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4952250	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4952252	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs55730514	0.88[ASN][1000 genomes]
rs62142079	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62142080	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67157050	0.80[ASN][1000 genomes]
rs6723154	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap]
rs6725184	0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs6737500	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6748621	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6752375	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6758024	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6760105	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs678251	0.81[ASN][1000 genomes]
rs72862234	0.80[ASN][1000 genomes]
rs7370704	0.81[ASN][1000 genomes]
rs7561519	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs7566162	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7572964	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7573543	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7575139	0.80[ASN][1000 genomes]
rs7577696	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7581340	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs7586448	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7601267	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7605242	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7608127	0.80[ASN][1000 genomes]
rs7608229	0.80[ASN][1000 genomes]
rs9752651	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv873777	chr2:32019747-32197123	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10439444	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32099600-32193000	Weak transcription	Hela-S3	cervix
2	chr2:32117000-32205200	Weak transcription	NH-A	brain
3	chr2:32127400-32190200	Weak transcription	Lung	lung
4	chr2:32136600-32188800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:32137000-32189200	Weak transcription	Fetal Kidney	kidney
6	chr2:32145200-32190800	Weak transcription	Pancreas	Pancrea
7	chr2:32167200-32193200	Weak transcription	HSMM	muscle
8	chr2:32168200-32185000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:32168200-32189600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:32168200-32194400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:32168200-32197400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:32168400-32186200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:32168400-32186400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:32168400-32189400	Weak transcription	Fetal Intestine Small	intestine
15	chr2:32168400-32193600	Weak transcription	Fetal Brain Female	brain
16	chr2:32168400-32194200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:32168400-32202000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:32168400-32205200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:32168400-32205800	Weak transcription	Fetal Lung	lung
20	chr2:32168400-32205800	Weak transcription	Thymus	Thymus
21	chr2:32168400-32212200	Weak transcription	Esophagus	oesophagus
22	chr2:32168400-32233400	Weak transcription	Fetal Stomach	stomach
23	chr2:32168600-32187000	Weak transcription	Fetal Intestine Large	intestine
24	chr2:32168600-32187200	Weak transcription	Fetal Thymus	thymus
25	chr2:32168600-32193400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:32168800-32190000	Weak transcription	Dnd41	blood
27	chr2:32168800-32193200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:32170800-32185000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:32171000-32227600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:32171200-32198800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:32171400-32192600	Weak transcription	Osteobl	bone
32	chr2:32172200-32186000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:32173000-32184200	Weak transcription	K562	blood
34	chr2:32173200-32187800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:32181200-32185200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr2:32181600-32185400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:32182200-32185400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:32182400-32184000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:32182400-32184000	Enhancers	HMEC	breast
40	chr2:32182400-32184400	Flanking Active TSS	GM12878-XiMat	blood
41	chr2:32182400-32184600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:32182400-32185200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:32182400-32185400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:32182600-32184200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:32182600-32184400	Enhancers	NHEK	skin
46	chr2:32182600-32184600	Enhancers	Primary B cells from peripheral blood	blood
47	chr2:32182600-32187600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:32182600-32187800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:32182800-32183800	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr2:32182800-32183800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links