Variant report

Variant	rs4663540
Chromosome Location	chr2:234259470-234259471
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	SIN3AK20	chr2:234259300-234259802	A549	lung:	n/a	n/a
2	CTCF	chr2:234259400-234259550	HCFaa	heart:	n/a	n/a
3	MAX	chr2:234259256-234259760	Hela-S3	cervix:	n/a	chr2:234259570-234259579
4	FOS	chr2:234259351-234259777	K562	blood:	n/a	chr2:234259568-234259579 chr2:234259569-234259578 chr2:234259556-234259567 chr2:234259568-234259580
5	TEAD4	chr2:234259213-234259964	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:234259025-234259916	A549	lung:	n/a	chr2:234259568-234259577 chr2:234259393-234259404 chr2:234259571-234259580
7	CTCF	chr2:234259420-234259570	HRPEpiC	eye:	n/a	n/a
8	NR3C1	chr2:234259415-234259759	A549	lung:	n/a	chr2:234259498-234259512
9	NR3C1	chr2:234259333-234259741	A549	lung:	n/a	chr2:234259498-234259512
10	GATA3	chr2:234259283-234259890	MCF-7	breast:	n/a	chr2:234259568-234259577 chr2:234259393-234259404 chr2:234259571-234259580
11	KAP1	chr2:234259252-234259830	HEK293	kidney:	n/a	n/a
12	MYC	chr2:234259025-234259812	NB4	blood:	n/a	chr2:234259570-234259579
13	EP300	chr2:234259319-234259768	Hela-S3	cervix:	n/a	chr2:234259570-234259579
14	CEBPB	chr2:234259275-234259791	Hela-S3	cervix:	n/a	n/a
15	E2F4	chr2:234259388-234259785	MCF10A-Er-Src	breast:	n/a	n/a
16	TFAP2C	chr2:234259207-234259804	Hela-S3	cervix:	n/a	chr2:234259512-234259527
17	CTCF	chr2:234259400-234259550	HEEpiC	esophagus:	n/a	n/a
18	MYC	chr2:234259440-234259690	MCF-7	breast:	n/a	chr2:234259570-234259579
19	CTCF	chr2:234259320-234259470	HFF	foreskin:	n/a	n/a
20	JUND	chr2:234259351-234259737	HepG2	liver:	n/a	chr2:234259569-234259578 chr2:234259568-234259579 chr2:234259568-234259580 chr2:234259556-234259567
21	YY1	chr2:234259394-234259620	K562	blood:	n/a	chr2:234259501-234259509
22	HCFC1	chr2:234259379-234259889	K562	blood:	n/a	n/a
23	CTCF	chr2:234259360-234259510	AG04450	lung:	n/a	n/a
24	POLR2A	chr2:234259217-234259932	U87	brain:	n/a	n/a
25	SMARCC1	chr2:234259185-234259795	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr2:234259387-234259669	K562	blood:	n/a	n/a
27	FOSL2	chr2:234259122-234259914	SK-N-SH	brain:	n/a	chr2:234259569-234259578 chr2:234259568-234259580
28	MAX	chr2:234259396-234259637	K562	blood:	n/a	chr2:234259570-234259579
29	CUX1	chr2:234259411-234259726	K562	blood:	n/a	n/a
30	CTCF	chr2:234259420-234259570	NHEK	skin:	n/a	n/a
31	FOSL2	chr2:234259196-234259902	MCF-7	breast:	n/a	chr2:234259569-234259578 chr2:234259568-234259580
32	SMC3	chr2:234259214-234259828	Hela-S3	cervix:	n/a	n/a
33	MAZ	chr2:234259308-234259782	K562	blood:	n/a	chr2:234259570-234259579
34	STAT3	chr2:234259351-234260392	MCF10A-Er-Src	breast:	n/a	chr2:234259389-234259400 chr2:234259557-234259566
35	CTCF	chr2:234259460-234259610	AoAF	blood vessel:	n/a	n/a
36	CTCF	chr2:234259460-234259610	AG10803	skin:	n/a	n/a
37	MYC	chr2:234259356-234259718	Hela-S3	cervix:	n/a	chr2:234259570-234259579
38	CTCF	chr2:234259420-234259570	AG04449	skin:	n/a	n/a
39	CTCF	chr2:234259460-234259610	AG04449	skin:	n/a	n/a
40	POLR2A	chr2:234259270-234259768	SK-N-SH	brain:	n/a	n/a
41	RAD21	chr2:234259319-234259811	Hela-S3	cervix:	n/a	chr2:234259497-234259509
42	PBX3	chr2:234259267-234259844	SK-N-SH	brain:	n/a	n/a
43	MYC	chr2:234259360-234259836	MCF10A-Er-Src	breast:	n/a	chr2:234259570-234259579
44	TFAP2A	chr2:234259207-234259808	Hela-S3	cervix:	n/a	chr2:234259512-234259527
45	NR3C1	chr2:234259318-234259731	A549	lung:	n/a	chr2:234259498-234259512
46	RAD21	chr2:234259348-234259759	SK-N-SH_RA	brain:	n/a	chr2:234259497-234259509
47	FOSL2	chr2:234259071-234260407	A549	lung:	n/a	chr2:234259569-234259578 chr2:234259568-234259580
48	SRF	chr2:234259099-234259871	HCT-116	colon:	n/a	n/a
49	CTCF	chr2:234259440-234259590	HCPEpiC	choroid plexus:	n/a	n/a
50	KAP1	chr2:234259061-234260406	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234257933..234260937-chr2:234261415..234264229,3	K562	blood:
2	chr2:234258654..234260896-chr2:234262665..234264444,3	MCF-7	breast:
3	chr2:234259457..234261123-chr2:234261520..234263458,2	MCF-7	breast:
4	chr2:234243954..234247958-chr2:234256896..234259564,3	MCF-7	breast:
5	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:
6	chr2:234196279..234198158-chr2:234258001..234260532,2	MCF-7	breast:
7	chr2:234223100..234224098-chr2:234259138..234259923,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243637	TF binding region
DGKD	TF binding region
ENSG00000251791	Chromatin interaction
ENSG00000259793	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000130561	Chromatin interaction
ENSG00000243637	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2971868	0.92[CEU][hapmap]
rs34339006	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7422272	0.91[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs838707	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs838710	0.80[AMR][1000 genomes]
rs838713	0.88[CEU][hapmap]
rs838714	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs838715	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs838719	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs838722	0.96[CEU][hapmap]
rs838730	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs838731	0.91[CEU][hapmap];0.81[GIH][hapmap]
rs838732	0.91[CEU][hapmap]
rs838733	0.92[CEU][hapmap]
rs838734	0.92[CEU][hapmap]
rs838735	0.91[CEU][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	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4663540	SP100	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234255000-234260000	Enhancers	Liver	Liver
2	chr2:234255800-234262400	Weak transcription	Right Atrium	heart
3	chr2:234256200-234260800	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:234256400-234260400	Enhancers	Fetal Intestine Small	intestine
5	chr2:234256400-234262400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr2:234256600-234259800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:234256600-234261400	Enhancers	Primary B cells from cord blood	blood
8	chr2:234256800-234262400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:234257000-234262200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:234257200-234260000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr2:234257200-234260400	Enhancers	Primary hematopoietic stem cells	blood
12	chr2:234257400-234260400	Enhancers	Fetal Intestine Large	intestine
13	chr2:234257600-234260000	Enhancers	Stomach Mucosa	stomach
14	chr2:234257600-234260400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:234257800-234259800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:234257800-234260000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:234257800-234260400	Enhancers	K562	blood
18	chr2:234257800-234263000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr2:234258000-234260200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:234258000-234260400	Enhancers	HSMM	muscle
21	chr2:234258000-234261800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:234258200-234259600	Enhancers	Brain Hippocampus Middle	brain
23	chr2:234258200-234259600	Enhancers	Colonic Mucosa	Colon
24	chr2:234258200-234259800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:234258200-234260000	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:234258200-234260000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:234258200-234260200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr2:234258200-234260800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:234258200-234261200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:234258200-234261800	Weak transcription	Esophagus	oesophagus
31	chr2:234258200-234261800	Weak transcription	Lung	lung
32	chr2:234258200-234262000	Weak transcription	Right Ventricle	heart
33	chr2:234258200-234262600	Weak transcription	Psoas Muscle	Psoas
34	chr2:234258400-234259600	Enhancers	GM12878-XiMat	blood
35	chr2:234258400-234260400	Enhancers	Brain Anterior Caudate	brain
36	chr2:234258400-234261000	Enhancers	NHEK	skin
37	chr2:234258400-234261800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:234258400-234261800	Weak transcription	Gastric	stomach
39	chr2:234258400-234261800	Weak transcription	Thymus	Thymus
40	chr2:234258400-234262000	Enhancers	Duodenum Mucosa	Duodenum
41	chr2:234258400-234262200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr2:234258400-234262400	Weak transcription	Ovary	ovary
43	chr2:234258600-234260200	Enhancers	HepG2	liver
44	chr2:234258600-234260400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:234258600-234261400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:234258600-234261800	Weak transcription	Spleen	Spleen
47	chr2:234258600-234262000	Weak transcription	Adipose Nuclei	Adipose
48	chr2:234258600-234262000	Weak transcription	Brain Substantia Nigra	brain
49	chr2:234258600-234262200	Weak transcription	Primary T cells from cord blood	blood
50	chr2:234258600-234262400	Weak transcription	Fetal Kidney	kidney

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