Variant report

Variant	rs413722
Chromosome Location	chr6:33398620-33398621
allele	A/G
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	RELA	chr6:33398109-33398898	GM19193	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
2	SP1	chr6:33398595-33399136	A549	lung:	n/a	chr6:33398918-33398930 chr6:33398874-33398888 chr6:33398918-33398930 chr6:33398919-33398928 chr6:33398919-33398933 chr6:33398919-33398928 chr6:33398920-33398929 chr6:33398936-33398957
3	STAT3	chr6:33398317-33398917	GM12878	blood:	n/a	n/a
4	RELA	chr6:33398068-33398938	GM18505	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
5	MXI1	chr6:33398550-33399322	GM12878	blood:	n/a	chr6:33398901-33398916
6	RELA	chr6:33398007-33399061	GM18951	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
7	KAP1	chr6:33398288-33398833	K562	blood:	n/a	n/a
8	RELA	chr6:33398026-33398970	GM10847	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
9	POLR2A	chr6:33398042-33399915	SK-N-MC	brain:	n/a	n/a
10	RELA	chr6:33397963-33399236	GM19099	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
11	SP1	chr6:33398587-33399145	A549	lung:	n/a	chr6:33398918-33398930 chr6:33398874-33398888 chr6:33398918-33398930 chr6:33398919-33398928 chr6:33398919-33398933 chr6:33398919-33398928 chr6:33398920-33398929 chr6:33398936-33398957
12	MAZ	chr6:33398235-33399507	IMR90	lung:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399420-33399430 chr6:33399300-33399311
13	ELF1	chr6:33398562-33399232	MCF-7	breast:	n/a	chr6:33398973-33398985 chr6:33398859-33398872
14	FOXM1	chr6:33398500-33399142	GM12878	blood:	n/a	n/a
15	RUNX3	chr6:33398575-33399064	GM12878	blood:	n/a	n/a
16	RELA	chr6:33398098-33399128	GM15510	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
17	ZNF143	chr6:33398557-33398912	K562	blood:	n/a	n/a
18	ELF1	chr6:33398592-33399081	HepG2	liver:	n/a	chr6:33398973-33398985 chr6:33398859-33398872
19	ELF1	chr6:33398445-33399141	MCF-7	breast:	n/a	chr6:33398973-33398985 chr6:33398859-33398872
20	ELF1	chr6:33398557-33399227	K562	blood:	n/a	chr6:33398973-33398985 chr6:33398859-33398872
21	EBF1	chr6:33398158-33398915	GM12878	blood:	n/a	chr6:33398371-33398382
22	ELF1	chr6:33398570-33399002	K562	blood:	n/a	chr6:33398973-33398985 chr6:33398859-33398872
23	POLR2A	chr6:33398547-33399564	PFSK-1	brain:	n/a	n/a
24	RELA	chr6:33397899-33398943	GM12878	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
25	POLR2A	chr6:33398112-33400875	H1-hESC	embryonic stem cell:	n/a	n/a
26	MXI1	chr6:33398438-33399602	SK-N-SH	brain:	n/a	chr6:33399483-33399492 chr6:33398901-33398916 chr6:33399333-33399342
27	GABPA	chr6:33398600-33399130	MCF-7	breast:	n/a	n/a
28	RELA	chr6:33398015-33399018	GM12891	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
29	YY1	chr6:33398618-33399497	H1-hESC	embryonic stem cell:	n/a	chr6:33398973-33398987 chr6:33398996-33399008
30	MTA3	chr6:33397969-33399774	GM12878	blood:	n/a	n/a
31	PAX5	chr6:33398478-33399135	GM12878	blood:	n/a	n/a
32	ELF1	chr6:33398620-33399181	GM12878	blood:	n/a	chr6:33398973-33398985 chr6:33398859-33398872

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33398610-33398660	HUVEC	blood vessel:	n/a
2	chr6:33398610-33398660	HNPCEpiC	eye:	n/a
3	chr6:33398610-33398660	RPTEC	kidney:	n/a
4	chr6:33398610-33398660	MCF-7	breast:	n/a
5	chr6:33398610-33398660	HCT-116	colon:	n/a
6	chr6:33398610-33398660	HepG2	liver:	n/a
7	chr6:33398610-33398660	SK-N-SH_RA	brain:	n/a
8	chr6:33398610-33398660	GM12891	blood:	n/a
9	chr6:33398610-33398660	PrEC	prostate:	n/a
10	chr6:33398610-33398660	T-47D	breast:	n/a
11	chr6:33398610-33398660	AG04449	skin:	fetal
12	chr6:33398610-33398660	Jurkat	blood:	n/a
13	chr6:33398610-33398660	GM06990	blood:	n/a
14	chr6:33398610-33398660	U87	brain:	n/a
15	chr6:33398610-33398660	HPAEpiC	pulmonary alveolar:	n/a
16	chr6:33398610-33398660	H1-hESC	embryonic stem cell:	embryo
17	chr6:33398610-33398660	AG04450	lung:	fetal
18	chr6:33398610-33398660	Hela-S3	cervix:	n/a
19	chr6:33398610-33398660	NB4	blood:	n/a
20	chr6:33398610-33398660	HRE	kidney:	n/a
21	chr6:33398610-33398660	PFSK-1	brain:	n/a
22	chr6:33398610-33398660	SK-N-MC	brain:	n/a
23	chr6:33398610-33398660	SKMC	muscle:	n/a
24	chr6:33398610-33398660	AoSMC	blood vessel:	n/a
25	chr6:33398610-33398660	GM12878	blood:	n/a
26	chr6:33398610-33398660	Hepatocyte	liver:	n/a
27	chr6:33398610-33398660	NHDF-neo	bronchial:	n/a
28	chr6:33398610-33398660	SK-N-SH	brain:	n/a
29	chr6:33398610-33398660	AG09309	skin:	n/a
30	chr6:33398610-33398660	HAEpiC	amniotic membrane:	n/a
31	chr6:33398610-33398660	AG09319	gingival:	n/a
32	chr6:33398610-33398660	ovcar-3	ovarian:	n/a
33	chr6:33398610-33398660	HIPEpiC	eye:	n/a
34	chr6:33398610-33398660	HCF	heart:	n/a
35	chr6:33398610-33398660	HRCEpiC	kidney:	n/a
36	chr6:33398610-33398660	HMEC	breast:	n/a
37	chr6:33398610-33398660	NH-A	brain:	n/a
38	chr6:33398610-33398660	HL-60	blood:	n/a
39	chr6:33398610-33398660	GM19239	blood:	n/a
40	chr6:33398610-33398660	BE2_C	brain:	n/a
41	chr6:33398610-33398660	HCPEpiC	choroid plexus:	n/a
42	chr6:33398610-33398660	Caco-2	colon:	n/a
43	chr6:33398610-33398660	IMR90	lung:	fetal
44	chr6:33398610-33398660	HEEpiC	esophagus:	n/a
45	chr6:33398610-33398660	HCM	heart:	n/a
46	chr6:33398610-33398660	AG10803	skin:	n/a
47	chr6:33398610-33398660	K562	blood:	n/a
48	chr6:33398610-33398660	HRPEpiC	eye:	n/a
49	chr6:33398610-33398660	CMK	blood:	n/a
50	chr6:33398610-33398660	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr6:33263619..33269524-chr6:33392449..33400505,13	K562	blood:
3	chr6:33395899..33401993-chr6:33420102..33423796,11	MCF-7	breast:
4	chr6:33174005..33176257-chr6:33398590..33400783,2	MCF-7	breast:
5	chr6:33395342..33398838-chr6:33677022..33679442,4	K562	blood:
6	chr6:33358270..33361160-chr6:33397889..33401606,4	K562	blood:
7	chr6:33173944..33176266-chr6:33397713..33400457,2	K562	blood:
8	chr6:33392449..33400629-chr6:33419013..33424035,12	MCF-7	breast:
9	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
10	chr6:33254824..33258515-chr6:33394130..33398725,7	K562	blood:
11	chr6:33396539..33398732-chr6:33463165..33465539,2	K562	blood:
12	chr6:33244147..33247113-chr6:33398461..33400467,3	K562	blood:
13	chr6:33394932..33398976-chr6:33412593..33416199,4	MCF-7	breast:
14	chr6:33357884..33361160-chr6:33397889..33401606,5	K562	blood:

Variant related genes	Relation type
SYNGAP1	TF binding region
SYNGAP1	CpG island
ENSG00000227057	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000231925	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1755040	0.81[AMR][1000 genomes]
rs210131	0.81[EUR][1000 genomes]
rs210190	0.85[AMR][1000 genomes]
rs2747476	1.00[ASN][1000 genomes]
rs28800551	0.85[AMR][1000 genomes]
rs3119019	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119021	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119022	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3119024	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3119025	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119026	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3119027	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130023	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130024	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130026	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130032	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130035	0.85[EUR][1000 genomes]
rs35432298	0.85[AMR][1000 genomes]
rs35700288	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35796955	0.85[AMR][1000 genomes]
rs35817932	0.85[AMR][1000 genomes]
rs36003672	0.85[AMR][1000 genomes]
rs406009	1.00[ASN][1000 genomes]
rs421328	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs4713634	0.81[EUR][1000 genomes]
rs498066	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910721	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs761582	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762843	0.91[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv932196	chr6:33383131-33400706	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
6	nsv1019212	chr6:33398031-33413930	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33396000-33401400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:33396200-33399200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:33396200-33399800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr6:33396200-33400000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr6:33396200-33400000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr6:33396200-33400200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr6:33396200-33400200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr6:33396200-33400400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr6:33396200-33400400	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:33396400-33398800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:33396400-33398800	Enhancers	Brain Substantia Nigra	brain
12	chr6:33396400-33398800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr6:33396400-33399000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:33396400-33399000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:33396400-33399200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:33396400-33401200	Enhancers	Spleen	Spleen
17	chr6:33396400-33401600	Enhancers	Fetal Heart	heart
18	chr6:33396400-33403000	Weak transcription	Ovary	ovary
19	chr6:33396400-33405200	Weak transcription	Psoas Muscle	Psoas
20	chr6:33396600-33398800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:33396600-33398800	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:33396600-33399000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:33396600-33399000	Enhancers	Colon Smooth Muscle	Colon
24	chr6:33396600-33399200	Enhancers	Fetal Intestine Small	intestine
25	chr6:33396600-33399200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr6:33396600-33399400	Enhancers	HMEC	breast
27	chr6:33396600-33399600	Enhancers	Liver	Liver
28	chr6:33396600-33399600	Enhancers	Fetal Intestine Large	intestine
29	chr6:33396600-33399600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr6:33396600-33400600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr6:33396600-33400600	Enhancers	Fetal Muscle Leg	muscle
32	chr6:33396600-33400600	Enhancers	Lung	lung
33	chr6:33396600-33400800	Weak transcription	Right Atrium	heart
34	chr6:33396600-33401000	Weak transcription	HSMMtube	muscle
35	chr6:33396600-33416000	Weak transcription	Pancreas	Pancrea
36	chr6:33396800-33398800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:33396800-33398800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr6:33396800-33398800	Enhancers	Stomach Smooth Muscle	stomach
39	chr6:33396800-33399000	Enhancers	Fetal Stomach	stomach
40	chr6:33396800-33399200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:33396800-33399800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:33396800-33402000	Enhancers	Fetal Lung	lung
43	chr6:33396800-33403000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:33396800-33403000	Weak transcription	Aorta	Aorta
45	chr6:33397000-33399400	Enhancers	NHEK	skin
46	chr6:33397200-33399600	Enhancers	HUVEC	blood vessel
47	chr6:33397200-33399800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr6:33397200-33400800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr6:33397400-33398800	Weak transcription	Colonic Mucosa	Colon
50	chr6:33397400-33398800	Weak transcription	Left Ventricle	heart

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