Variant report

Variant	rs2796552
Chromosome Location	chr10:43362298-43362299
allele	C/T
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	ZC3H11A	chr10:43362273-43362323	K562	blood:	n/a	n/a
2	CTCF	chr10:43362098-43362480	GM12878	blood:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
3	CTCF	chr10:43362200-43362350	GM12878	blood:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
4	CTCF	chr10:43362260-43362410	HRPEpiC	eye:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
5	CTCF	chr10:43362260-43362410	Hela-S3	cervix:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
6	CTCF	chr10:43362171-43362407	LNCaP	prostate:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
7	MYC	chr10:43362091-43362469	A549	lung:	n/a	n/a
8	CTCF	chr10:43362160-43362450	HCM	heart:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
9	MAX	chr10:43361750-43362546	A549	lung:	n/a	n/a
10	SMC3	chr10:43362118-43362476	K562	blood:	n/a	chr10:43362285-43362299 chr10:43362262-43362270
11	CHD2	chr10:43362228-43362397	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr10:43362157-43362442	MCF-7	breast:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
13	CTCF	chr10:43362260-43362410	GM12866	blood:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
14	RFX5	chr10:43362259-43362461	Hela-S3	cervix:	n/a	n/a
15	MYC	chr10:43362251-43362436	MCF-7	breast:	n/a	n/a
16	CTCF	chr10:43362220-43362370	HBMEC	blood vessel:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
17	CTCF	chr10:43362240-43362390	GM12867	blood:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
18	CTCF	chr10:43362180-43362450	NHLF	lung:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
19	MAZ	chr10:43362163-43362482	K562	blood:	n/a	n/a
20	CTCF	chr10:43362240-43362390	AG10803	skin:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
21	EP300	chr10:43362207-43362489	SK-N-SH_RA	brain:	n/a	chr10:43362313-43362329
22	CTCF	chr10:43362240-43362390	GM12865	blood:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
23	CTCF	chr10:43362160-43362310	NHEK	skin:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
24	CTCF	chr10:43362220-43362370	GM12874	blood:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
25	CTCF	chr10:43362110-43362425	LNCaP	prostate:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
26	CTCF	chr10:43362260-43362410	HPF	lung:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
27	RAD21	chr10:43361944-43362582	MCF-7	breast:	n/a	chr10:43362284-43362303 chr10:43362285-43362299 chr10:43362385-43362398
28	CTCF	chr10:43362220-43362370	NHEK	skin:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
29	CTCF	chr10:43362220-43362370	HA-sp	spinal cord:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
30	CTCF	chr10:43362206-43362382	HepG2	liver:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
31	CTCF	chr10:43362113-43362525	MCF-7	breast:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
32	ZNF143	chr10:43362257-43362442	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:43362236-43362454	IMR90	lung:	n/a	n/a
34	CTCF	chr10:43362240-43362390	NHDF-neo	bronchial:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
35	CTCF	chr10:43362198-43362392	MCF-7	breast:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
36	YY1	chr10:43362170-43362492	H1-hESC	embryonic stem cell:	n/a	chr10:43362315-43362329
37	RAD21	chr10:43362027-43362593	ECC-1	luminal epithelium:	n/a	chr10:43362284-43362303 chr10:43362285-43362299 chr10:43362385-43362398
38	USF2	chr10:43362229-43362375	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr10:43362260-43362410	BJ	skin:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
40	CTCF	chr10:43362240-43362390	HFF-Myc	foreskin:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
41	CTCF	chr10:43362240-43362390	WI-38	lung:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
42	MAX	chr10:43362183-43362402	K562	blood:	n/a	n/a
43	RAD21	chr10:43362119-43362533	MCF-7	breast:	n/a	chr10:43362284-43362303 chr10:43362285-43362299 chr10:43362385-43362398
44	CTCF	chr10:43362220-43362370	Hela-S3	cervix:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300
45	ELF1	chr10:43362190-43362436	K562	blood:	n/a	chr10:43362315-43362327
46	ZNF143	chr10:43362166-43362486	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chr10:43362155-43362536	ECC-1	luminal epithelium:	n/a	n/a
48	MAX	chr10:43362184-43362419	H1-hESC	embryonic stem cell:	n/a	n/a
49	HDAC2	chr10:43361452-43362542	MCF-7	breast:	n/a	n/a
50	CTCF	chr10:43362220-43362370	HUVEC	blood vessel:	n/a	chr10:43362283-43362301 chr10:43362286-43362299 chr10:43362285-43362306 chr10:43362284-43362300

No.	Distal block	Cell Line	Cell type
1	chr10:43360364..43363685-chr10:43571830..43575400,3	MCF-7	breast:
2	chr10:43361867..43362389-chr10:43470791..43471531,2	K562	blood:
3	chr10:43361133..43364035-chr10:43632950..43635001,2	MCF-7	breast:
4	chr10:43361928..43362761-chr10:43600658..43601529,2	MCF-7	breast:
5	chr10:43355311..43356829-chr10:43360308..43362900,2	MCF-7	breast:
6	chr10:43361913..43362690-chr10:43470789..43471679,3	MCF-7	breast:
7	chr10:43360509..43362298-chr10:43627787..43629550,2	MCF-7	breast:
8	chr10:43361921..43363073-chr10:43574052..43574909,5	MCF-7	breast:
9	chr10:43361782..43362789-chr10:43574108..43574983,3	K562	blood:
10	chr10:43361871..43362799-chr10:43470867..43471733,6	MCF-7	breast:
11	chr10:43360554..43363791-chr10:43570974..43576100,9	MCF-7	breast:
12	chr10:43361854..43362671-chr10:43600633..43601533,4	K562	blood:

Variant related genes	Relation type
ENSG00000234944	TF binding region
ENSG00000165731	Chromatin interaction
ENSG00000273008	Chromatin interaction
ENSG00000169826	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1815715	0.87[ASN][1000 genomes]
rs1815718	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1815720	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1815721	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092265	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142989	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744068	0.87[ASN][1000 genomes]
rs2744074	0.88[ASN][1000 genomes]
rs2744079	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795506	0.90[ASN][1000 genomes]
rs2796554	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2796556	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2796557	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2796558	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2796559	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2796560	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796561	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2796577	0.87[ASN][1000 genomes]
rs3121276	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3121277	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788243	0.96[ASN][1000 genomes]
rs788246	0.81[ASN][1000 genomes]
rs788247	0.95[ASN][1000 genomes]
rs788249	0.95[ASN][1000 genomes]
rs788284	0.96[ASN][1000 genomes]
rs788285	0.99[ASN][1000 genomes]
rs788287	0.99[ASN][1000 genomes]
rs788288	0.98[ASN][1000 genomes]
rs788289	0.98[ASN][1000 genomes]
rs788292	0.90[ASN][1000 genomes]
rs788293	0.98[ASN][1000 genomes]
rs947546	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv1047838	chr10:43234590-43379219	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv947892	chr10:43358233-43368929	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43361400-43362600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:43361400-43362600	Bivalent/Poised TSS	Fetal Brain Female	brain
3	chr10:43361600-43362400	Enhancers	Primary B cells from cord blood	blood
4	chr10:43361600-43362400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
5	chr10:43361600-43362400	Active TSS	Right Ventricle	heart
6	chr10:43361600-43362600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr10:43361600-43362600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:43361600-43362600	Enhancers	Pancreas	Pancrea
9	chr10:43361600-43362600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
10	chr10:43361800-43362400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr10:43361800-43362400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:43361800-43362400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:43361800-43362400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
14	chr10:43361800-43362600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr10:43361800-43362600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:43362000-43362400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr10:43362000-43362400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:43362000-43362400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
19	chr10:43362000-43362400	Active TSS	Brain Hippocampus Middle	brain
20	chr10:43362000-43362600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
21	chr10:43362000-43362600	Active TSS	Brain Cingulate Gyrus	brain
22	chr10:43362000-43362600	Bivalent Enhancer	Fetal Stomach	stomach
23	chr10:43362200-43362400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr10:43362200-43362400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr10:43362200-43362400	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
26	chr10:43362200-43362400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr10:43362200-43362400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:43362200-43362400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:43362200-43362400	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr10:43362200-43362400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr10:43362200-43362400	Enhancers	NHDF-Ad	bronchial
32	chr10:43362200-43362600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:43362200-43362600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:43362200-43362600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr10:43362200-43362600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr10:43362200-43362600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr10:43362200-43362600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr10:43362200-43362600	Bivalent Enhancer	Adipose Nuclei	Adipose
39	chr10:43362200-43362600	Enhancers	Brain Angular Gyrus	brain
40	chr10:43362200-43362600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
41	chr10:43362200-43362600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr10:43362200-43362600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr10:43362200-43362600	Bivalent Enhancer	Fetal Brain Male	brain
44	chr10:43362200-43362600	Bivalent Enhancer	Fetal Intestine Small	intestine
45	chr10:43362200-43362600	Bivalent Enhancer	Fetal Lung	lung
46	chr10:43362200-43362600	Bivalent Enhancer	Placenta	Placenta
47	chr10:43362200-43362600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
48	chr10:43362200-43362600	Bivalent Enhancer	Rectal Smooth Muscle	rectum
49	chr10:43362200-43362600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
50	chr10:43362200-43362600	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links