Variant report

Variant	rs2954019
Chromosome Location	chr8:126477759-126477760
allele	A/G
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	NFIC	chr8:126477653-126478496	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr8:126477659-126479594	ECC-1	luminal epithelium:	n/a	chr8:126479568-126479577
3	TCF12	chr8:126477683-126479561	ECC-1	luminal epithelium:	n/a	chr8:126478959-126478967 chr8:126479277-126479286
4	NFIC	chr8:126477500-126478461	ECC-1	luminal epithelium:	n/a	n/a
5	ZMIZ1	chr8:126477732-126477765	K562	blood:	n/a	n/a
6	RCOR1	chr8:126477628-126477827	Hela-S3	cervix:	n/a	n/a
7	ZNF143	chr8:126477622-126477773	K562	blood:	n/a	n/a
8	RCOR1	chr8:126477643-126477766	K562	blood:	n/a	n/a
9	TCF12	chr8:126477753-126478523	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:126476379..126479143-chr8:126667265..126669380,2	MCF-7	breast:
2	chr8:126442745..126445381-chr8:126476232..126477978,2	MCF-7	breast:
3	chr8:126465262..126466889-chr8:126476635..126478328,2	MCF-7	breast:
4	chr8:126472290..126473943-chr8:126475663..126477931,2	MCF-7	breast:
5	chr8:126459529..126461149-chr8:126475843..126477879,2	K562	blood:

Variant related genes	Relation type
ENSG00000253111	TF binding region
ENSG00000173334	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10808545	0.81[JPT][hapmap]
rs10808546	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17321515	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2001844	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2001945	0.85[CEU][hapmap]
rs2954021	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2954022	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2954029	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2954031	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs2980853	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2980854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980860	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2980868	0.96[EUR][1000 genomes]
rs2980869	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2980871	0.96[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2980875	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2980882	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2980886	0.95[EUR][1000 genomes]
rs6982636	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6999569	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891437	chr8:126470817-126629328	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126464800-126478000	Weak transcription	Gastric	stomach
2	chr8:126465200-126477800	Weak transcription	Fetal Heart	heart
3	chr8:126472400-126479000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:126475400-126479200	Weak transcription	A549	lung
5	chr8:126475600-126477800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr8:126475600-126478000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr8:126475600-126478200	Weak transcription	HepG2	liver
8	chr8:126475600-126478800	Weak transcription	K562	blood
9	chr8:126475800-126479600	Enhancers	Placenta	Placenta
10	chr8:126476400-126478800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr8:126476400-126479000	Weak transcription	Right Ventricle	heart
12	chr8:126476600-126478000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:126476600-126478800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:126476600-126478800	Enhancers	Hela-S3	cervix
15	chr8:126476600-126479000	Weak transcription	Liver	Liver
16	chr8:126476600-126483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:126476800-126477800	Weak transcription	HSMM	muscle
18	chr8:126476800-126479000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:126476800-126479200	Weak transcription	NHEK	skin
20	chr8:126477000-126479800	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr8:126477200-126479800	Enhancers	HUVEC	blood vessel
22	chr8:126477400-126479400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr8:126477400-126479600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:126477400-126485000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr8:126477600-126478800	Enhancers	Fetal Kidney	kidney
26	chr8:126477600-126479400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:126477600-126479400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr8:126477600-126479400	Enhancers	Adipose Nuclei	Adipose
29	chr8:126477600-126479400	Enhancers	Fetal Stomach	stomach
30	chr8:126477600-126479400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr8:126477600-126479400	Enhancers	Spleen	Spleen
32	chr8:126477600-126479600	Enhancers	Fetal Muscle Leg	muscle
33	chr8:126477600-126479600	Enhancers	NH-A	brain
34	chr8:126477600-126479800	Enhancers	Fetal Lung	lung
35	chr8:126477600-126480000	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links