Variant report

Variant	rs6717209
Chromosome Location	chr2:32393949-32393950
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr2:32393649-32394034	K562	blood:	n/a	n/a
2	GATA2	chr2:32393590-32394038	K562	blood:	n/a	n/a
3	POLR2A	chr2:32393635-32394015	K562	blood:	n/a	n/a
4	PAX5	chr2:32393585-32393956	GM12892	blood:	n/a	chr2:32393681-32393690
5	JUND	chr2:32393623-32394050	K562	blood:	n/a	n/a
6	PAX5	chr2:32393506-32393977	GM12891	blood:	n/a	chr2:32393681-32393690
7	PAX5	chr2:32393511-32394053	GM12878	blood:	n/a	chr2:32393681-32393690
8	PML	chr2:32393613-32394105	K562	blood:	n/a	n/a
9	NR2F2	chr2:32393529-32394116	K562	blood:	n/a	n/a
10	RCOR1	chr2:32393654-32394037	K562	blood:	n/a	n/a
11	POLR2A	chr2:32393577-32394060	HepG2	liver:	n/a	n/a
12	NFIC	chr2:32393512-32394054	GM12878	blood:	n/a	n/a
13	EP300	chr2:32393617-32394057	GM12878	blood:	n/a	n/a
14	EP300	chr2:32393592-32394043	K562	blood:	n/a	n/a
15	POLR2A	chr2:32393543-32394089	PBDE	blood:	n/a	n/a
16	MTA3	chr2:32393526-32394133	GM12878	blood:	n/a	n/a
17	BHLHE40	chr2:32393691-32393966	K562	blood:	n/a	n/a
18	NR2F2	chr2:32393605-32393998	K562	blood:	n/a	n/a
19	IRF1	chr2:32393620-32394172	K562	blood:	n/a	chr2:32393681-32393695 chr2:32393689-32393700 chr2:32393681-32393691 chr2:32394069-32394076
20	TAL1	chr2:32393606-32394078	K562	blood:	n/a	n/a
21	CBX3	chr2:32393663-32394072	K562	blood:	n/a	n/a
22	EP300	chr2:32393554-32394090	K562	blood:	n/a	n/a
23	RUNX3	chr2:32393533-32394033	GM12878	blood:	n/a	n/a
24	ZMIZ1	chr2:32393666-32394027	K562	blood:	n/a	n/a
25	TEAD4	chr2:32393588-32394065	K562	blood:	n/a	n/a
26	MAFF	chr2:32393678-32394055	K562	blood:	n/a	n/a
27	PML	chr2:32393583-32394032	K562	blood:	n/a	n/a
28	TEAD4	chr2:32393552-32394090	K562	blood:	n/a	n/a
29	ARID3A	chr2:32393621-32394178	K562	blood:	n/a	n/a
30	MXI1	chr2:32393573-32393985	K562	blood:	n/a	n/a
31	IRF1	chr2:32393610-32394022	K562	blood:	n/a	chr2:32393681-32393695 chr2:32393689-32393700 chr2:32393681-32393691
32	GATA1	chr2:32393569-32394206	PBDE	blood:	n/a	n/a
33	POLR2A	chr2:32393576-32394454	K562	blood:	n/a	n/a
34	CUX1	chr2:32393736-32394016	K562	blood:	n/a	n/a
35	PAX5	chr2:32393611-32393950	GM12878	blood:	n/a	chr2:32393681-32393690
36	TBL1XR1	chr2:32393577-32394090	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:32393662..32395511-chr2:32603984..32606045,2	K562	blood:
2	chr2:32393531..32396327-chr2:32515532..32517225,2	K562	blood:
3	chr2:32393475..32396085-chr2:32440047..32443005,2	K562	blood:
4	chr2:32233185..32238105-chr2:32388775..32395245,11	K562	blood:
5	chr2:32233077..32237611-chr2:32388376..32395245,10	K562	blood:
6	chr2:32234481..32236468-chr2:32392692..32395377,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272716	TF binding region
ENSG00000230046	Chromatin interaction
ENSG00000162959	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10172468	0.85[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10208246	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10490360	1.00[CHB][hapmap]
rs11124274	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11124275	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11124278	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11676475	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11676938	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11678119	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs11683760	0.82[ASN][1000 genomes]
rs11683842	0.82[ASN][1000 genomes]
rs11694630	0.89[ASN][1000 genomes]
rs12465124	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12465351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12474598	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12614686	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12989936	1.00[CHB][hapmap]
rs12995952	0.85[ASN][1000 genomes]
rs12997026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017189	1.00[CHB][hapmap]
rs13022197	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs13427170	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13431540	0.80[AMR][1000 genomes]
rs177083	0.96[CEU][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs17767988	1.00[CHB][hapmap]
rs212679	0.91[JPT][hapmap];0.81[YRI][hapmap]
rs212686	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs212687	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs212694	0.89[EUR][1000 genomes]
rs212703	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs212704	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs212706	0.83[CEU][hapmap]
rs212707	0.81[CEU][hapmap]
rs212708	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs212713	1.00[CEU][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs212715	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs212716	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs212717	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs212738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212739	1.00[CHB][hapmap];0.96[JPT][hapmap];0.97[ASN][1000 genomes]
rs212740	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs212741	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212743	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs212744	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs212745	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs212746	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs212748	1.00[CEU][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212749	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs212752	0.81[EUR][1000 genomes]
rs212753	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs212755	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212757	0.93[EUR][1000 genomes]
rs212760	0.91[JPT][hapmap]
rs212762	0.95[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs216544	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2280967	1.00[CHB][hapmap]
rs2280973	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2365555	1.00[CHB][hapmap]
rs2366736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2886393	0.84[ASN][1000 genomes]
rs34976640	0.84[ASN][1000 genomes]
rs3752916	1.00[CHB][hapmap];0.96[JPT][hapmap]
rs3752917	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3769602	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs3769603	0.81[ASN][1000 genomes]
rs3769604	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3769606	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs385076	0.83[CHB][hapmap]
rs3851308	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3851310	0.81[ASN][1000 genomes]
rs4258846	0.97[ASN][1000 genomes]
rs435572	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4407291	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs443609	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4519572	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs467523	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs479333	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4952209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4952248	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4952250	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4952252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55877106	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56208031	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62134021	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs659239	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6716179	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6723154	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6725184	0.87[CHB][hapmap]
rs6737500	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6748621	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6752375	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs6758024	1.00[CHB][hapmap]
rs6760105	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6761417	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72863940	0.81[AMR][1000 genomes]
rs7561519	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7566162	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7572964	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7573543	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs7577696	1.00[CHB][hapmap]
rs7581340	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7581432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7586448	1.00[CHB][hapmap]
rs7588883	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7592239	0.86[ASN][1000 genomes]
rs7592356	0.84[ASN][1000 genomes]
rs7601267	1.00[CHB][hapmap]
rs7604289	0.81[ASN][1000 genomes]
rs7605242	1.00[CHB][hapmap];0.87[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6717209	NLRC4	cis	Lymphoblastoid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391400-32401800	Weak transcription	Spleen	Spleen
2	chr2:32391400-32402000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:32391400-32402000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:32391600-32397200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr2:32391600-32397400	Weak transcription	Left Ventricle	heart
6	chr2:32391600-32401800	Weak transcription	Gastric	stomach
7	chr2:32391600-32402000	Weak transcription	Esophagus	oesophagus
8	chr2:32391600-32402800	Weak transcription	Lung	lung
9	chr2:32391600-32403400	Weak transcription	Aorta	Aorta
10	chr2:32391600-32406600	Weak transcription	Small Intestine	intestine
11	chr2:32391600-32409600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:32391600-32426400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:32391800-32394600	Weak transcription	Right Atrium	heart
15	chr2:32391800-32396800	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:32391800-32397200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:32391800-32397200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:32391800-32397600	Weak transcription	Fetal Thymus	thymus
19	chr2:32391800-32397600	Weak transcription	Ovary	ovary
20	chr2:32391800-32397800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:32391800-32400200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:32391800-32400200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:32391800-32401800	Weak transcription	Brain Substantia Nigra	brain
24	chr2:32391800-32409600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:32391800-32431400	Weak transcription	Stomach Mucosa	stomach
26	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
27	chr2:32392000-32395600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:32392000-32397000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:32392000-32397000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:32392000-32397000	Weak transcription	Primary T cells from cord blood	blood
31	chr2:32392000-32397000	Weak transcription	Fetal Brain Female	brain
32	chr2:32392000-32397000	Weak transcription	NH-A	brain
33	chr2:32392000-32397200	Weak transcription	Primary B cells from cord blood	blood
34	chr2:32392000-32397200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:32392000-32397200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr2:32392000-32397400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:32392000-32397600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:32392000-32397600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:32392000-32397600	Weak transcription	HMEC	breast
40	chr2:32392000-32397800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:32392000-32397800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:32392000-32398200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:32392000-32401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:32392000-32401800	Weak transcription	Brain Angular Gyrus	brain
45	chr2:32392000-32401800	Weak transcription	Fetal Stomach	stomach
46	chr2:32392000-32402000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:32392000-32402000	Weak transcription	Fetal Lung	lung
48	chr2:32392000-32402000	Weak transcription	Thymus	Thymus
49	chr2:32392000-32402200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:32392000-32403600	Weak transcription	Fetal Kidney	kidney

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