Variant report

Variant	rs2583277
Chromosome Location	chr12:104388291-104388292
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104375830..104377503-chr12:104387925..104389874,3	K562	blood:
2	chr12:104384261..104388673-chr12:104456948..104460032,3	K562	blood:
3	chr12:104388056..104390327-chr12:104394417..104397045,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1177458	0.83[EUR][1000 genomes]
rs12369883	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs172814	0.83[EUR][1000 genomes]
rs2254063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254064	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2576973	0.81[EUR][1000 genomes]
rs2583227	0.83[EUR][1000 genomes]
rs2583251	0.83[EUR][1000 genomes]
rs2583260	0.83[EUR][1000 genomes]
rs2583263	0.83[EUR][1000 genomes]
rs2583271	1.00[ASN][1000 genomes]
rs2629768	0.83[EUR][1000 genomes]
rs2629770	0.82[EUR][1000 genomes]
rs2629771	0.83[EUR][1000 genomes]
rs2629779	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629793	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629804	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2700510	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700515	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722169	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2722171	1.00[ASN][1000 genomes]
rs2723845	1.00[ASN][1000 genomes]
rs2723846	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723847	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723868	1.00[ASN][1000 genomes]
rs2723876	0.82[EUR][1000 genomes]
rs322102	0.81[EUR][1000 genomes]
rs322105	0.83[EUR][1000 genomes]
rs322106	0.83[EUR][1000 genomes]
rs322107	0.83[EUR][1000 genomes]
rs322108	0.83[EUR][1000 genomes]
rs322110	0.83[EUR][1000 genomes]
rs784081	0.83[EUR][1000 genomes]
rs796736	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2583277	KRTHB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104362000-104392800	Weak transcription	Fetal Brain Male	brain
2	chr12:104377800-104390200	Weak transcription	Fetal Heart	heart
3	chr12:104377800-104391000	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:104377800-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:104380800-104391400	Weak transcription	Ovary	ovary
6	chr12:104380800-104395600	Weak transcription	Aorta	Aorta
7	chr12:104380800-104400200	Weak transcription	NHLF	lung
8	chr12:104381000-104388400	Weak transcription	Spleen	Spleen
9	chr12:104381000-104389000	Weak transcription	Thymus	Thymus
10	chr12:104381000-104390600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:104381000-104390800	Weak transcription	K562	blood
12	chr12:104381000-104391200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:104381000-104391200	Weak transcription	Right Ventricle	heart
14	chr12:104381000-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:104381600-104392800	Weak transcription	Left Ventricle	heart
16	chr12:104382600-104389000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:104383600-104389600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:104384800-104390800	Weak transcription	Fetal Lung	lung
19	chr12:104385000-104390800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:104385000-104400200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:104385400-104400200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:104385600-104390800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:104385600-104404000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:104385800-104400200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:104386000-104388800	Weak transcription	Osteobl	bone
26	chr12:104387000-104400200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:104387200-104388800	Enhancers	HSMM	muscle
28	chr12:104387200-104404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:104387400-104390400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:104387400-104391400	Weak transcription	Fetal Stomach	stomach
31	chr12:104387800-104388600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:104387800-104388600	Enhancers	HSMMtube	muscle
33	chr12:104388000-104388400	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr12:104388000-104388400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:104388200-104388600	Enhancers	Psoas Muscle	Psoas
36	chr12:104388200-104389200	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links