Variant report

Variant	rs9287734
Chromosome Location	chr2:11724475-11724476
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	ATF3	chr2:11724353-11724581	K562	blood:	n/a	n/a
2	MYC	chr2:11724282-11724685	NB4	blood:	n/a	chr2:11724458-11724467 chr2:11724457-11724466
3	CTCF	chr2:11724460-11724610	NHLF	lung:	n/a	chr2:11724557-11724575
4	CTCF	chr2:11724442-11724682	MCF-7	breast:	n/a	chr2:11724557-11724575
5	ZMIZ1	chr2:11724395-11724763	K562	blood:	n/a	n/a
6	RCOR1	chr2:11724377-11724718	HepG2	liver:	n/a	n/a
7	EGR1	chr2:11724142-11724804	MCF-7	breast:	n/a	chr2:11724443-11724456 chr2:11724444-11724458 chr2:11724442-11724457
8	RAD21	chr2:11724291-11724808	Hela-S3	cervix:	n/a	n/a
9	FOSL2	chr2:11724155-11724672	SK-N-SH	brain:	n/a	chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724455-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
10	CTCF	chr2:11724460-11724610	HRE	kidney:	n/a	chr2:11724557-11724575
11	ATF3	chr2:11724174-11724740	A549	lung:	n/a	n/a
12	CTCF	chr2:11724437-11724702	Fibrobl	skin:	n/a	chr2:11724557-11724575
13	MAFK	chr2:11724381-11724647	HepG2	liver:	n/a	n/a
14	CTCF	chr2:11724460-11724610	GM12874	blood:	n/a	chr2:11724557-11724575
15	EGR1	chr2:11724102-11724834	HCT-116	colon:	n/a	chr2:11724443-11724456 chr2:11724444-11724458 chr2:11724442-11724457
16	CTCF	chr2:11724396-11724738	GM12878	blood:	n/a	chr2:11724557-11724575
17	CTCF	chr2:11724451-11724696	ProgFib	skin:	n/a	chr2:11724557-11724575
18	EGR1	chr2:11724335-11724550	GM12878	blood:	n/a	chr2:11724443-11724456 chr2:11724444-11724458 chr2:11724442-11724457
19	FOS	chr2:11724208-11724687	MCF10A-Er-Src	breast:	n/a	chr2:11724456-11724468 chr2:11724418-11724429 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724456-11724467 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
20	CTCF	chr2:11724312-11724768	T-47D	breast:	n/a	chr2:11724557-11724575
21	RAD21	chr2:11724214-11724832	ECC-1	luminal epithelium:	n/a	n/a
22	NFIC	chr2:11724159-11724743	HepG2	liver:	n/a	n/a
23	MAFK	chr2:11724449-11724618	HepG2	liver:	n/a	n/a
24	RAD21	chr2:11724294-11724807	HepG2	liver:	n/a	n/a
25	MYC	chr2:11724409-11724730	K562	blood:	n/a	chr2:11724458-11724467 chr2:11724457-11724466
26	TBP	chr2:11724399-11724810	HepG2	liver:	n/a	n/a
27	CTCF	chr2:11724274-11724781	K562	blood:	n/a	chr2:11724557-11724575
28	CTCF	chr2:11724460-11724610	GM12870	blood:	n/a	chr2:11724557-11724575
29	FOXP2	chr2:11724387-11724664	SK-N-MC	brain:	n/a	n/a
30	YY1	chr2:11724373-11724641	GM12892	blood:	n/a	n/a
31	EP300	chr2:11724326-11724594	GM12878	blood:	n/a	chr2:11724457-11724466 chr2:11724458-11724467
32	CTCF	chr2:11724421-11724698	LNCaP	prostate:	n/a	chr2:11724557-11724575
33	RAD21	chr2:11724309-11724821	MCF-7	breast:	n/a	n/a
34	MXI1	chr2:11724319-11724661	GM12878	blood:	n/a	n/a
35	MEF2A	chr2:11724278-11724593	K562	blood:	n/a	n/a
36	MAX	chr2:11724249-11724658	K562	blood:	n/a	chr2:11724458-11724467 chr2:11724457-11724466
37	JUND	chr2:11724340-11724607	HepG2	liver:	n/a	chr2:11724456-11724467 chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
38	RAD21	chr2:11724327-11724749	GM12878	blood:	n/a	n/a
39	CTCF	chr2:11724337-11724746	K562	blood:	n/a	chr2:11724557-11724575
40	JUN	chr2:11724289-11724708	K562	blood:	n/a	chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
41	RAD21	chr2:11724267-11724815	MCF-7	breast:	n/a	n/a
42	E2F4	chr2:11724159-11724540	MCF10A-Er-Src	breast:	n/a	n/a
43	MAFF	chr2:11724368-11724744	K562	blood:	n/a	n/a
44	CHD2	chr2:11724422-11724716	HepG2	liver:	n/a	n/a
45	ZC3H11A	chr2:11724414-11724672	K562	blood:	n/a	n/a
46	CTCF	chr2:11724460-11724610	GM12865	blood:	n/a	chr2:11724557-11724575
47	MXI1	chr2:11724283-11724736	HepG2	liver:	n/a	n/a
48	CTCF	chr2:11724275-11724824	MCF-7	breast:	n/a	chr2:11724557-11724575
49	ZNF384	chr2:11724373-11724631	GM12878	blood:	n/a	n/a
50	CTCF	chr2:11724414-11724688	GM10248	blood:	n/a	chr2:11724557-11724575

No.	Distal block	Cell Line	Cell type
1	chr2:11272046..11273363-chr2:11723821..11725006,6	K562	blood:
2	chr2:11723075..11724603-chr2:11731951..11734172,2	MCF-7	breast:
3	chr2:11723582..11725102-chr2:11727716..11730148,2	K562	blood:
4	chr2:11557796..11559144-chr2:11724145..11724865,3	K562	blood:

Variant related genes	Relation type
RN7SL674P	TF binding region
GREB1	TF binding region
ENSG00000196208	Chromatin interaction
ENSG00000145063	Chromatin interaction
ENSG00000150873	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10165819	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200851	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929759	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11674184	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs11674605	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11679686	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12468019	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12470971	0.81[CHB][hapmap]
rs12993278	0.91[EUR][1000 genomes]
rs13016186	0.89[EUR][1000 genomes]
rs13017593	0.89[EUR][1000 genomes]
rs13394619	0.92[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1529868	0.80[JPT][hapmap]
rs16857668	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs1865573	0.87[ASN][1000 genomes]
rs2358040	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2884374	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4669752	0.92[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6746291	0.94[EUR][1000 genomes]
rs7576826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9678410	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9789414	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9798272	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS 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 miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11711600-11738600	Weak transcription	Left Ventricle	heart
5	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:11719200-11725800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:11719200-11738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:11720000-11735600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:11721600-11733000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:11721800-11726000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:11722000-11724600	Enhancers	Fetal Muscle Leg	muscle
14	chr2:11722000-11725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:11722200-11724600	Enhancers	Fetal Muscle Trunk	muscle
16	chr2:11722600-11724800	Enhancers	Stomach Smooth Muscle	stomach
17	chr2:11722600-11724800	Enhancers	HSMMtube	muscle
18	chr2:11722800-11724800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:11722800-11724800	Enhancers	Stomach Mucosa	stomach
20	chr2:11722800-11724800	Enhancers	NHDF-Ad	bronchial
21	chr2:11723000-11724600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:11723000-11724600	Enhancers	Brain Anterior Caudate	brain
23	chr2:11723000-11724800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:11723000-11724800	Enhancers	NH-A	brain
25	chr2:11723000-11725400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:11723000-11740400	Weak transcription	Liver	Liver
27	chr2:11723200-11724800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:11723200-11724800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:11723200-11724800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr2:11723200-11724800	Enhancers	Brain Angular Gyrus	brain
31	chr2:11723200-11724800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:11723200-11724800	Enhancers	Hela-S3	cervix
33	chr2:11723200-11735400	Weak transcription	Brain Substantia Nigra	brain
34	chr2:11723400-11725800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:11723400-11735200	Weak transcription	Fetal Lung	lung
36	chr2:11723400-11740000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:11723600-11724600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:11723600-11724600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:11723600-11724600	Genic enhancers	HepG2	liver
40	chr2:11723600-11735200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:11723600-11735600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:11723600-11738600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:11723800-11724800	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr2:11724000-11724600	Enhancers	Brain Hippocampus Middle	brain
45	chr2:11724000-11724800	Enhancers	Fetal Intestine Large	intestine
46	chr2:11724200-11724800	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:11724200-11725400	Weak transcription	Ovary	ovary
48	chr2:11724200-11732800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:11724200-11732800	Weak transcription	Pancreas	Pancrea
50	chr2:11724400-11724800	Bivalent Enhancer	K562	blood

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