Variant report

Variant	rs28501188
Chromosome Location	chr1:120259794-120259795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120257304..120259977-chr1:120266897..120269007,2	K562	blood:
2	chr1:120258475..120260260-chr1:120263404..120265007,2	K562	blood:
3	chr1:120251114..120252823-chr1:120259616..120261697,2	K562	blood:
4	chr1:120259179..120261862-chr20:39488876..39490638,3	MCF-7	breast:
5	chr1:120189290..120192192-chr1:120258102..120260904,2	K562	blood:

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10218713	0.82[ASN][1000 genomes]
rs12057776	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1441011	0.81[ASN][1000 genomes]
rs1886736	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236398	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3790708	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60466603	0.81[ASN][1000 genomes]
rs6683122	0.82[ASN][1000 genomes]
rs894079	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs942835	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120256000-120263800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:120256200-120266600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:120256200-120267400	Weak transcription	Lung	lung
4	chr1:120256200-120271800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:120256400-120271800	Weak transcription	Gastric	stomach
6	chr1:120256400-120276800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
8	chr1:120256600-120263400	Weak transcription	Primary T cells from cord blood	blood
9	chr1:120256600-120275600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:120256800-120263800	Weak transcription	HUVEC	blood vessel
11	chr1:120256800-120266000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:120257000-120259800	Enhancers	Liver	Liver
13	chr1:120257000-120263800	Weak transcription	Aorta	Aorta
14	chr1:120257000-120266000	Weak transcription	HSMMtube	muscle
15	chr1:120257000-120271800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:120257000-120277400	Weak transcription	Fetal Heart	heart
17	chr1:120257000-120278400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:120257000-120278600	Weak transcription	HSMM	muscle
19	chr1:120257000-120282400	Weak transcription	A549	lung
20	chr1:120257200-120263200	Weak transcription	NHLF	lung
21	chr1:120257200-120287000	Weak transcription	NH-A	brain
22	chr1:120257600-120262000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:120257600-120263600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:120257600-120263600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:120257600-120263800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:120257600-120264400	Weak transcription	Placenta	Placenta
27	chr1:120257600-120268000	Weak transcription	Fetal Brain Male	brain
28	chr1:120258000-120261000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:120258400-120262000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:120258600-120260400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:120258600-120260800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:120258600-120263200	Weak transcription	HMEC	breast
33	chr1:120258600-120263400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:120258600-120263800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:120258600-120267200	Weak transcription	Fetal Brain Female	brain
36	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:120258800-120261000	Weak transcription	Ovary	ovary
38	chr1:120258800-120261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:120258800-120261600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:120258800-120263200	Weak transcription	Thymus	Thymus
41	chr1:120258800-120263400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:120258800-120263800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:120258800-120266000	Weak transcription	Esophagus	oesophagus
44	chr1:120258800-120269400	Weak transcription	Spleen	Spleen
45	chr1:120258800-120275000	Weak transcription	Right Atrium	heart
46	chr1:120259000-120262200	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:120259000-120262800	Weak transcription	Adipose Nuclei	Adipose
48	chr1:120259000-120263400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:120259000-120263400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:120259000-120263400	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links