Variant report

Variant	rs4973564
Chromosome Location	chr2:233718440-233718441
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	CTCF	chr2:233717635-233718693	HCT-116	colon:	n/a	chr2:233717998-233718011 chr2:233717995-233718013 chr2:233717998-233718011 chr2:233717997-233718018
2	SP1	chr2:233717882-233719350	HCT-116	colon:	n/a	n/a
3	FOSL1	chr2:233718010-233719300	HCT-116	colon:	n/a	chr2:233718707-233718714 chr2:233718930-233718941
4	CTCF	chr2:233717522-233718792	A549	lung:	n/a	chr2:233717998-233718011 chr2:233717995-233718013 chr2:233717998-233718011 chr2:233717997-233718018
5	SPI1	chr2:233717848-233718479	HL-60	blood:	n/a	chr2:233718284-233718293 chr2:233718285-233718292 chr2:233718283-233718296
6	SPI1	chr2:233718122-233718481	GM12891	blood:	n/a	chr2:233718284-233718293 chr2:233718285-233718292 chr2:233718283-233718296
7	RAD21	chr2:233717625-233718592	SK-N-SH	brain:	n/a	chr2:233717996-233718015
8	EGR1	chr2:233718262-233719362	HCT-116	colon:	n/a	n/a
9	KAP1	chr2:233718421-233719101	HEK293	kidney:	n/a	n/a
10	CEBPB	chr2:233718402-233719239	Hela-S3	cervix:	n/a	n/a
11	CBX3	chr2:233717726-233719180	HCT-116	colon:	n/a	chr2:233718033-233718044
12	CTCF	chr2:233718300-233718450	HPF	lung:	n/a	n/a
13	CTCF	chr2:233718400-233718550	HEEpiC	esophagus:	n/a	n/a
14	SMC3	chr2:233717409-233718596	SK-N-SH	brain:	n/a	chr2:233717997-233718011
15	RAD21	chr2:233717667-233718550	HCT-116	colon:	n/a	chr2:233717996-233718015
16	RAD21	chr2:233717655-233719354	HCT-116	colon:	n/a	chr2:233717996-233718015
17	EP300	chr2:233718146-233719327	A549	lung:	n/a	chr2:233719257-233719271
18	NFIC	chr2:233718249-233719369	ECC-1	luminal epithelium:	n/a	n/a
19	CTCF	chr2:233718320-233718470	NHDF-neo	bronchial:	n/a	n/a
20	NFIC	chr2:233718257-233719255	ECC-1	luminal epithelium:	n/a	n/a
21	TCF12	chr2:233718196-233719312	A549	lung:	n/a	n/a
22	KAP1	chr2:233718307-233719087	U2OS	brain:	n/a	n/a
23	SMC3	chr2:233717601-233719414	Hela-S3	cervix:	n/a	chr2:233717997-233718011
24	JUND	chr2:233718397-233719209	K562	blood:	n/a	chr2:233718707-233718714 chr2:233718930-233718941
25	ARID3A	chr2:233717938-233719055	K562	blood:	n/a	n/a
26	JUND	chr2:233717813-233719338	HCT-116	colon:	n/a	chr2:233718707-233718714 chr2:233718930-233718941

No.	Distal block	Cell Line	Cell type
1	chr2:233717760..233718460-chr2:234159678..234160599,3	MCF-7	breast:
2	chr2:233716839..233718860-chr2:233720640..233722784,2	K562	blood:
3	chr2:233717471..233718489-chr2:234159703..234160491,4	K562	blood:
4	chr2:233717958..233718532-chr2:233918679..233919191,2	MCF-7	breast:

Variant related genes	Relation type
C2orf82	TF binding region
ENSG00000085978	Chromatin interaction
ENSG00000182600	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10205801	0.84[MEX][hapmap]
rs10210953	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1078323	0.92[CEU][hapmap]
rs1083522	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10933406	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1104764	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11688166	0.88[CEU][hapmap]
rs11689851	0.88[CEU][hapmap]
rs12105766	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs12619195	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13007579	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs13008436	0.84[EUR][1000 genomes]
rs13009957	0.83[EUR][1000 genomes]
rs13024330	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs13029336	0.83[JPT][hapmap]
rs1515961	0.83[JPT][hapmap]
rs17164	0.88[CEU][hapmap]
rs1973675	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs2289911	0.88[CEU][hapmap]
rs2344613	0.88[CEU][hapmap]
rs2675953	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2675954	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs2675968	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2675972	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs283470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs283473	0.83[JPT][hapmap]
rs4973563	0.88[CEU][hapmap]
rs6704763	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs6717048	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6733495	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs709937	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.94[ASN][1000 genomes]
rs737027	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs748002	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs7560115	0.80[EUR][1000 genomes]
rs778341	0.80[ASW][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs778370	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs778371	0.81[AFR][1000 genomes]
rs921055	0.88[CEU][hapmap]
rs938569	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]

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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233689200-233726400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:233698400-233723600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:233701000-233729200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr2:233703400-233718600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:233703400-233726400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:233703400-233726600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:233703600-233725200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr2:233703800-233724800	Strong transcription	Dnd41	blood
11	chr2:233704000-233721400	Strong transcription	Fetal Intestine Large	intestine
12	chr2:233704200-233719200	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:233704200-233725000	Strong transcription	Fetal Thymus	thymus
14	chr2:233704400-233726200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:233704400-233726600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:233704600-233726000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:233704600-233728000	Strong transcription	Primary T cells from cord blood	blood
18	chr2:233704800-233719000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:233704800-233726600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:233705000-233726600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:233705600-233726600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:233705600-233727800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:233712000-233721400	Strong transcription	Fetal Intestine Small	intestine
24	chr2:233712000-233728200	Strong transcription	Fetal Stomach	stomach
25	chr2:233713400-233721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:233713600-233721600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:233714000-233726400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:233714600-233720000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:233714800-233721400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:233714800-233721400	Weak transcription	Fetal Brain Male	brain
31	chr2:233715200-233721200	Weak transcription	Right Ventricle	heart
32	chr2:233715200-233721400	Weak transcription	Stomach Mucosa	stomach
33	chr2:233715800-233721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:233715800-233725400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:233716000-233720000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:233716000-233720200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:233716000-233721200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:233716200-233720200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:233716600-233718600	Genic enhancers	K562	blood
40	chr2:233716600-233719600	Genic enhancers	HSMM	muscle
41	chr2:233716800-233719800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:233716800-233720000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:233716800-233720000	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:233716800-233720000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:233716800-233720200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:233716800-233720800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:233716800-233721000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:233717000-233718600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:233717000-233718600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:233717000-233718800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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