Variant report

Variant	rs6541124
Chromosome Location	chr1:220218466-220218467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:220009776..220012687-chr1:220217353..220218943,2	K562	blood:
2	chr1:220215698..220221065-chr1:220265352..220268996,5	K562	blood:
3	chr1:220138957..220140569-chr1:220217050..220219686,2	K562	blood:
4	chr1:220190580..220193578-chr1:220217938..220219443,2	K562	blood:
5	chr1:220218169..220221765-chr1:220261064..220269153,11	MCF-7	breast:
6	chr1:220217537..220219750-chr1:220295098..220297083,2	K562	blood:
7	chr1:220214211..220216766-chr1:220216909..220219452,2	MCF-7	breast:
8	chr1:220209718..220212778-chr1:220216575..220219154,4	K562	blood:
9	chr1:220215698..220219502-chr1:220266015..220268343,4	K562	blood:
10	chr1:220218207..220221672-chr1:220261461..220265020,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPRS-1	chr1:220218325-220218488	NONHSAT009572

No data

Variant related genes	Relation type
ENSG00000162813	Chromatin interaction
ENSG00000067704	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11806086	1.00[TSI][hapmap]
rs2808027	1.00[TSI][hapmap]
rs36122746	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs41274788	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs41304103	0.93[ASN][1000 genomes]
rs5030752	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs5030754	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6683340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690630	0.89[CHB][hapmap]
rs6704420	0.87[EUR][1000 genomes]
rs7517173	0.81[AFR][1000 genomes];0.93[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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription 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 miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv3388149	chr1:220205606-220233828	Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220170400-220218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:220172600-220218600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:220178200-220218600	Weak transcription	Right Ventricle	heart
4	chr1:220193600-220218600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:220203400-220218600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:220206800-220219000	Weak transcription	Fetal Lung	lung
7	chr1:220210600-220218600	Weak transcription	Right Atrium	heart
8	chr1:220213400-220218600	Weak transcription	Left Ventricle	heart
9	chr1:220213400-220218600	Weak transcription	Psoas Muscle	Psoas
10	chr1:220213400-220218600	Weak transcription	Thymus	Thymus
11	chr1:220213400-220219000	Weak transcription	Ovary	ovary
12	chr1:220213400-220219200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:220213400-220219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:220213400-220219400	Weak transcription	Spleen	Spleen
15	chr1:220213600-220218600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:220213600-220218600	Weak transcription	Fetal Kidney	kidney
17	chr1:220213600-220218600	Weak transcription	HSMMtube	muscle
18	chr1:220213600-220219000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:220213800-220218600	Weak transcription	Placenta	Placenta
20	chr1:220213800-220218600	Weak transcription	Fetal Thymus	thymus
21	chr1:220213800-220218800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:220214200-220218600	Weak transcription	Esophagus	oesophagus
23	chr1:220214800-220218600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:220215600-220218800	Weak transcription	Fetal Stomach	stomach
25	chr1:220216200-220218600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr1:220216400-220218800	Enhancers	Fetal Intestine Large	intestine
27	chr1:220216600-220218600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:220216800-220218600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:220216800-220218600	Transcr. at gene 5' and 3'	K562	blood
30	chr1:220216800-220218800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr1:220216800-220218800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:220217000-220218600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:220217000-220218600	Enhancers	HUVEC	blood vessel
34	chr1:220217200-220218600	Enhancers	Gastric	stomach
35	chr1:220217400-220218600	Weak transcription	Brain Germinal Matrix	brain
36	chr1:220217400-220220800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:220217600-220218600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr1:220217600-220218600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:220217600-220218600	Enhancers	Lung	lung
40	chr1:220217600-220219000	Flanking Active TSS	Dnd41	blood
41	chr1:220217800-220218800	Flanking Active TSS	Hela-S3	cervix
42	chr1:220217800-220219000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:220217800-220220400	Active TSS	Aorta	Aorta
44	chr1:220218000-220218600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr1:220218000-220218800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:220218000-220218800	Flanking Active TSS	NHEK	skin
47	chr1:220218000-220219000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:220218000-220219000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr1:220218000-220219000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:220218000-220219000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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