Variant report

Variant	rs11892788
Chromosome Location	chr2:54784108-54784109
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	RUNX3	chr2:54783601-54784119	GM12878	blood:	n/a	n/a
2	MXI1	chr2:54783677-54788216	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr2:54783724-54784508	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr2:54783662-54784211	SK-N-SH	brain:	n/a	n/a
5	RCOR1	chr2:54784035-54784199	K562	blood:	n/a	n/a
6	EBF1	chr2:54784016-54785230	GM12878	blood:	n/a	n/a
7	CEBPB	chr2:54783937-54784201	Hela-S3	cervix:	n/a	n/a
8	EP300	chr2:54783756-54784187	SK-N-SH_RA	brain:	n/a	n/a
9	POLR2A	chr2:54782355-54786484	HepG2	liver:	n/a	n/a
10	CEBPB	chr2:54783837-54784248	IMR90	lung:	n/a	n/a
11	MXI1	chr2:54783574-54784218	GM12878	blood:	n/a	n/a
12	PBX3	chr2:54783741-54784189	SK-N-SH	brain:	n/a	n/a
13	EP300	chr2:54783726-54784410	SK-N-SH_RA	brain:	n/a	n/a
14	ZNF263	chr2:54784107-54788614	HEK293-T-REx	kidney:	n/a	chr2:54786455-54786464 chr2:54787545-54787554 chr2:54785640-54785649 chr2:54785523-54785532 chr2:54786989-54786998
15	STAT1	chr2:54783880-54786368	Hela-S3	cervix:	n/a	chr2:54784890-54784899 chr2:54784736-54784747 chr2:54784889-54784900 chr2:54785850-54785862 chr2:54784721-54784729 chr2:54784891-54784900 chr2:54784888-54784902
16	POLR2A	chr2:54783785-54784148	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54197301..54199396-chr2:54783418..54785695,2	MCF-7	breast:
2	chr2:54783297..54785333-chr2:54809031..54810704,2	K562	blood:
3	chr2:54772020..54776106-chr2:54782775..54785505,4	K562	blood:
4	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
5	chr2:54782515..54784267-chr2:54820223..54822640,2	MCF-7	breast:
6	chr2:54782460..54784855-chr2:54875341..54877678,2	K562	blood:

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000170634	Chromatin interaction
ENSG00000234943	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000237887	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10165490	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs10180713	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1047499	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11885703	0.84[EUR][1000 genomes]
rs11898012	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs12104998	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12105792	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12468469	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12617036	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713260	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13016942	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13399435	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs1367295	0.81[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1541854	0.94[EUR][1000 genomes]
rs17344044	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs17344072	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17521078	0.81[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1864493	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292356	0.89[EUR][1000 genomes]
rs2292357	0.85[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2941586	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2941587	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2941591	0.81[EUR][1000 genomes]
rs2941595	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2971877	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2971879	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3106204	0.83[EUR][1000 genomes]
rs354231	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs3796014	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4233952	0.84[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4455199	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4592889	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671221	0.81[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671222	0.82[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671225	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671226	0.86[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671945	0.82[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671946	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671947	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671949	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671951	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671954	0.89[ASN][1000 genomes]
rs4671955	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671956	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4990319	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545411	0.90[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545413	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545414	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545415	0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6545418	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6545419	0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6545427	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545429	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545434	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6704769	0.82[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs6706372	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs6724590	0.85[EUR][1000 genomes]
rs6729826	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6731661	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6732949	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6734658	0.94[EUR][1000 genomes]
rs6735813	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6742607	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6746016	0.82[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6746306	0.85[EUR][1000 genomes]
rs6748816	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6761369	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6761398	0.81[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7563706	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7589236	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7607451	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs907135	0.86[CEU][hapmap];0.84[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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54777600-54784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:54777600-54784800	Weak transcription	Aorta	Aorta
3	chr2:54777800-54784200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:54778000-54784200	Weak transcription	Fetal Brain Male	brain
5	chr2:54779200-54784200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:54779400-54784200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:54779400-54784200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:54779800-54784200	Enhancers	NHDF-Ad	bronchial
9	chr2:54779800-54784600	Enhancers	Right Ventricle	heart
10	chr2:54780800-54784400	Enhancers	Primary T cells from cord blood	blood
11	chr2:54781000-54784600	Enhancers	Fetal Intestine Small	intestine
12	chr2:54781000-54784800	Enhancers	Right Atrium	heart
13	chr2:54781200-54784200	Weak transcription	K562	blood
14	chr2:54781200-54784600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr2:54781400-54784400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:54781400-54784400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr2:54781400-54784800	Enhancers	Left Ventricle	heart
18	chr2:54781600-54784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:54781800-54784600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:54781800-54784600	Enhancers	Adipose Nuclei	Adipose
21	chr2:54781800-54784600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:54781800-54784600	Enhancers	Fetal Intestine Large	intestine
23	chr2:54781800-54784800	Enhancers	Brain Anterior Caudate	brain
24	chr2:54782000-54784200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:54782000-54784400	Enhancers	Colon Smooth Muscle	Colon
26	chr2:54782000-54784800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:54782000-54784800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:54782000-54784800	Weak transcription	Psoas Muscle	Psoas
29	chr2:54782200-54784400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:54782200-54784600	Enhancers	HMEC	breast
31	chr2:54782200-54784600	Enhancers	HUVEC	blood vessel
32	chr2:54782200-54784800	Enhancers	Pancreas	Pancrea
33	chr2:54782200-54785600	Enhancers	Fetal Heart	heart
34	chr2:54782400-54784200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:54782400-54784200	Enhancers	GM12878-XiMat	blood
36	chr2:54782400-54784600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:54782400-54784600	Enhancers	NHLF	lung
38	chr2:54782400-54784800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:54782400-54784800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:54782400-54784800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:54782400-54784800	Enhancers	HSMM	muscle
42	chr2:54782600-54784400	Enhancers	Small Intestine	intestine
43	chr2:54782600-54784400	Enhancers	NH-A	brain
44	chr2:54782600-54784600	Enhancers	Fetal Thymus	thymus
45	chr2:54782600-54784800	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:54782600-54785000	Enhancers	Brain Angular Gyrus	brain
47	chr2:54782800-54784600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:54782800-54784600	Enhancers	Stomach Smooth Muscle	stomach
49	chr2:54782800-54784800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:54782800-54784800	Enhancers	Brain Hippocampus Middle	brain

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