Variant report

Variant	rs13021958
Chromosome Location	chr2:55753758-55753759
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	SPI1	chr2:55753279-55753763	HL-60	blood:	n/a	chr2:55753509-55753518 chr2:55753508-55753521 chr2:55753507-55753520 chr2:55753510-55753517

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55751187..55754186-chr2:55756755..55759283,2	MCF-7	breast:

Variant related genes	Relation type
CCDC104	TF binding region
ENSG00000163001	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1013138	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12617627	0.92[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12618859	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs12619903	0.90[YRI][hapmap]
rs12986444	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12986797	0.82[AFR][1000 genomes]
rs12992408	0.92[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12993624	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs12998780	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12999506	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12999680	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12999966	0.90[YRI][hapmap]
rs13001425	0.84[YRI][hapmap]
rs13003270	0.82[EUR][1000 genomes]
rs13005678	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13006502	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13009239	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13009447	0.83[YRI][hapmap]
rs13009906	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13010217	0.92[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13014898	0.93[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015018	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13015030	0.93[CEU][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13015744	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13018767	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13025331	0.92[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13027095	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13027803	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13032503	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1318672	1.00[CEU][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1443746	0.81[YRI][hapmap]
rs1822513	0.84[YRI][hapmap]
rs34013926	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34143512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35124901	0.82[AFR][1000 genomes]
rs3791654	0.92[CEU][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4322879	0.95[YRI][hapmap]
rs5012561	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs55888859	0.85[AMR][1000 genomes]
rs56122729	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs66545054	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737995	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs6757006	0.95[YRI][hapmap];0.93[ASN][1000 genomes]
rs7575170	0.90[YRI][hapmap]
rs8080	0.92[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55757600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:55748000-55761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:55748000-55761200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
7	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
8	chr2:55748200-55756600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:55748200-55757200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:55748200-55757200	Weak transcription	Brain Angular Gyrus	brain
11	chr2:55748200-55757200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:55748200-55757400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:55748200-55764600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:55748200-55764600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:55748200-55765000	Weak transcription	K562	blood
16	chr2:55748200-55769600	Weak transcription	Small Intestine	intestine
17	chr2:55748200-55769600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:55748200-55772000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:55748200-55773000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:55748200-55775800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:55748200-55777400	Weak transcription	NHLF	lung
22	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
23	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:55748400-55761400	Weak transcription	NHEK	skin
25	chr2:55748400-55764400	Weak transcription	GM12878-XiMat	blood
26	chr2:55748400-55772200	Weak transcription	HMEC	breast
27	chr2:55748600-55770000	Weak transcription	Dnd41	blood
28	chr2:55749400-55754400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:55749400-55758600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:55749600-55758800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:55749600-55760000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:55749800-55754000	Strong transcription	Brain Anterior Caudate	brain
33	chr2:55749800-55756800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr2:55750000-55775400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:55750400-55760400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:55750600-55754000	Strong transcription	Osteobl	bone
37	chr2:55750600-55755400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:55750600-55760200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:55750800-55753800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:55750800-55753800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:55750800-55753800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:55750800-55753800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr2:55750800-55753800	Strong transcription	NHDF-Ad	bronchial
44	chr2:55750800-55754000	Strong transcription	Brain Hippocampus Middle	brain
45	chr2:55750800-55754200	Strong transcription	Fetal Thymus	thymus
46	chr2:55750800-55754400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:55750800-55754400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:55750800-55754400	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr2:55750800-55754400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr2:55750800-55754600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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