Variant report

Variant	rs12993657
Chromosome Location	chr2:38754071-38754072
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38740787..38742664-chr2:38753203..38755236,2	MCF-7	breast:
2	chr2:38748763..38750578-chr2:38752263..38755021,2	K562	blood:
3	chr2:38754021..38756013-chr2:38969685..38972568,2	K562	blood:
4	chr2:38753350..38754887-chr2:38758237..38760009,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12105827	0.90[ASN][1000 genomes]
rs12622497	0.83[EUR][1000 genomes]
rs12622526	0.84[EUR][1000 genomes]
rs13003268	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13004207	0.90[EUR][1000 genomes]
rs13008970	0.99[ASN][1000 genomes]
rs13011825	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13017981	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13033060	0.91[EUR][1000 genomes]
rs13382384	0.83[EUR][1000 genomes]
rs13383838	0.83[EUR][1000 genomes]
rs17421378	0.82[ASN][1000 genomes]
rs17421399	0.90[ASN][1000 genomes]
rs17493321	0.89[ASN][1000 genomes]
rs34171322	0.87[ASN][1000 genomes]
rs34218951	0.86[ASN][1000 genomes]
rs34311924	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34355269	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34655983	0.97[ASN][1000 genomes]
rs35066504	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35120096	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35275207	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35299812	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35704960	0.97[ASN][1000 genomes]
rs35789272	0.97[ASN][1000 genomes]
rs35803605	0.87[ASN][1000 genomes]
rs3731843	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59239099	0.91[EUR][1000 genomes]
rs72795132	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574556	0.86[ASN][1000 genomes]
rs7584009	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7592090	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603200	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7606253	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606376	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv527492	chr2:38753337-38759797	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38750800-38755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:38750800-38755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:38751000-38755000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:38751000-38755000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:38751000-38755000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:38751200-38755000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:38751200-38762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:38751800-38754800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:38751800-38755200	Weak transcription	Aorta	Aorta
10	chr2:38751800-38755200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:38752200-38755000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:38752200-38755000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:38752200-38755000	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:38752200-38755000	Weak transcription	Psoas Muscle	Psoas
15	chr2:38752200-38755200	Weak transcription	Primary B cells from cord blood	blood
16	chr2:38752200-38755200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:38752200-38755400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:38752200-38760200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:38752400-38755000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:38752400-38755000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:38752600-38754400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:38752600-38754800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:38752800-38754600	Weak transcription	NHLF	lung
24	chr2:38753400-38754400	Enhancers	Adipose Nuclei	Adipose
25	chr2:38753400-38754800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:38753400-38755000	Weak transcription	NHDF-Ad	bronchial
27	chr2:38753600-38754600	Weak transcription	A549	lung
28	chr2:38753600-38755000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:38753800-38754600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:38753800-38754600	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:38753800-38754800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:38753800-38755000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:38753800-38755000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:38753800-38755000	Weak transcription	Osteobl	bone
35	chr2:38753800-38755200	Weak transcription	Liver	Liver
36	chr2:38753800-38755200	Weak transcription	Ovary	ovary
37	chr2:38754000-38754400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links