Variant report

Variant	rs3769602
Chromosome Location	chr2:32381829-32381830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32232439..32235784-chr2:32380849..32383379,3	K562	blood:
2	chr2:32367367..32371154-chr2:32378343..32385071,6	K562	blood:
3	chr2:32375856..32378077-chr2:32380295..32382033,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162959	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10172468	0.90[JPT][hapmap]
rs10208246	0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10439444	0.90[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10490360	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs11124274	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap]
rs11124275	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs11124276	0.80[AFR][1000 genomes]
rs11124278	0.89[ASN][1000 genomes]
rs11676938	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap]
rs11678119	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11681731	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11683760	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11683842	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11689817	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11691939	0.82[CEU][hapmap]
rs11694630	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12465351	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs12474598	0.88[ASN][1000 genomes]
rs12478134	0.82[CEU][hapmap]
rs12611678	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12614686	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12617289	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12618002	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12620922	0.80[AFR][1000 genomes]
rs12989936	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap]
rs12995952	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12997026	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs13006495	0.82[CEU][hapmap]
rs13007972	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13008192	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13017189	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[MKK][hapmap]
rs13022197	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap]
rs13427170	0.90[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs17011801	0.82[CEU][hapmap]
rs177082	0.82[CEU][hapmap]
rs17767988	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs212679	0.91[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs212687	0.82[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap]
rs212689	0.82[CEU][hapmap]
rs212699	0.87[GIH][hapmap]
rs212701	0.87[GIH][hapmap]
rs212703	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.84[ASN][1000 genomes]
rs212714	0.91[GIH][hapmap]
rs212715	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs212716	0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap]
rs212717	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap]
rs212727	0.93[GIH][hapmap]
rs212731	0.89[GIH][hapmap]
rs212737	0.86[GIH][hapmap]
rs212738	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs212739	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs212744	0.91[JPT][hapmap];0.86[AFR][1000 genomes]
rs212745	0.84[CEU][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs212746	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs212748	0.91[JPT][hapmap]
rs212751	0.82[CEU][hapmap]
rs212754	0.84[CEU][hapmap]
rs212755	0.91[JPT][hapmap]
rs212758	0.84[CEU][hapmap]
rs212759	0.84[CEU][hapmap]
rs212760	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs212762	0.95[JPT][hapmap]
rs216544	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap]
rs2280967	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.85[YRI][hapmap]
rs2280968	0.82[CEU][hapmap]
rs2280973	0.92[ASN][1000 genomes]
rs2294176	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2294179	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2365555	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap]
rs2365558	0.81[AMR][1000 genomes]
rs2366736	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2886393	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34197800	0.82[CEU][hapmap]
rs34976640	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35641550	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs375050	0.82[CEU][hapmap]
rs3752916	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769603	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3769604	0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs3769606	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap]
rs3851310	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4258846	0.88[ASN][1000 genomes]
rs430759	0.87[GIH][hapmap]
rs435572	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap]
rs4407291	0.93[ASN][1000 genomes]
rs443609	0.90[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap]
rs4519572	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs462878	0.82[CEU][hapmap]
rs467523	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs479333	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap]
rs4952209	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4952247	0.85[AFR][1000 genomes]
rs4952248	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4952250	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4952252	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs659239	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap]
rs6716179	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.90[ASN][1000 genomes]
rs6717209	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs6723154	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6725184	0.84[CEU][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap]
rs6737500	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.82[MKK][hapmap]
rs6748621	0.84[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6752375	0.85[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs6758024	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs6760105	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs7561519	0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap]
rs7566162	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs7572964	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7573543	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7577696	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap]
rs7581340	0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap]
rs7581432	0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7586448	0.90[CHB][hapmap]
rs7588883	0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.89[ASN][1000 genomes]
rs7592239	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7592356	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7601267	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap]
rs7604289	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7605242	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][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	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking 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	23 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3769602	NLRC4	cis	lymphoblastoid	seeQTL
rs3769602	NLRC4	cis	Lymphoblastoid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32331600-32390200	Weak transcription	Gastric	stomach
2	chr2:32331600-32390200	Weak transcription	Pancreas	Pancrea
3	chr2:32332800-32389400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:32333000-32389800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:32342200-32389800	Weak transcription	Aorta	Aorta
6	chr2:32344200-32389600	Weak transcription	HMEC	breast
7	chr2:32354600-32390200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:32354800-32389600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:32355000-32389800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:32355000-32390200	Weak transcription	Small Intestine	intestine
11	chr2:32355200-32383600	Weak transcription	HSMMtube	muscle
12	chr2:32355400-32389800	Weak transcription	HUVEC	blood vessel
13	chr2:32355600-32389600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:32355600-32389800	Weak transcription	Spleen	Spleen
15	chr2:32356400-32383200	Weak transcription	K562	blood
16	chr2:32357400-32389800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:32360000-32390200	Weak transcription	Ovary	ovary
18	chr2:32361000-32389800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:32361200-32383800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:32361200-32389600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:32361200-32389600	Weak transcription	NHEK	skin
22	chr2:32361200-32389600	Weak transcription	Osteobl	bone
23	chr2:32361400-32389600	Weak transcription	Fetal Heart	heart
24	chr2:32361400-32389600	Weak transcription	Hela-S3	cervix
25	chr2:32361600-32389600	Weak transcription	NH-A	brain
26	chr2:32363200-32389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:32363400-32386200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:32363400-32389800	Weak transcription	Fetal Kidney	kidney
29	chr2:32363600-32389800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:32365000-32389800	Weak transcription	Brain Anterior Caudate	brain
31	chr2:32367200-32389800	Weak transcription	Fetal Lung	lung
32	chr2:32367800-32389800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:32368200-32383000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:32369800-32389200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:32370000-32389400	Weak transcription	GM12878-XiMat	blood
36	chr2:32370000-32389600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:32370000-32389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr2:32370600-32389200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:32371000-32390200	Weak transcription	Left Ventricle	heart
40	chr2:32371000-32390200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:32371200-32389800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:32371400-32389400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr2:32371400-32389600	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:32371400-32389600	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:32371800-32389400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:32371800-32389600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:32371800-32389600	Weak transcription	Thymus	Thymus
48	chr2:32371800-32389800	Weak transcription	Right Ventricle	heart
49	chr2:32372200-32389800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:32372600-32389600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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