Variant report

Variant	rs2299040
Chromosome Location	chr6:15472669-15472670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15469193..15474455-chr6:15475135..15479397,6	K562	blood:
2	chr6:15397861..15400160-chr6:15471488..15473543,2	K562	blood:
3	chr6:15014502..15016184-chr6:15471465..15473973,2	K562	blood:
4	chr6:15247658..15249270-chr6:15471290..15473935,2	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1546851	1.00[ASN][1000 genomes]
rs2049950	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2049951	1.00[ASN][1000 genomes]
rs2049952	1.00[ASN][1000 genomes]
rs2064097	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064098	0.98[ASN][1000 genomes]
rs2064100	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2179167	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2179168	0.81[JPT][hapmap]
rs2237111	0.88[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2237112	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237114	0.93[ASN][1000 genomes]
rs2237115	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2237122	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2237125	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2237126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2237127	0.83[CHB][hapmap];1.00[ASN][1000 genomes]
rs2237128	1.00[ASN][1000 genomes]
rs2237129	1.00[ASN][1000 genomes]
rs2237130	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2237131	1.00[ASN][1000 genomes]
rs2237134	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2237135	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237136	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237143	0.81[JPT][hapmap]
rs2251828	1.00[ASN][1000 genomes]
rs2282818	0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2282822	1.00[ASN][1000 genomes]
rs2282824	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282826	0.87[GIH][hapmap]
rs2282827	0.87[GIH][hapmap]
rs2299037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2299038	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299041	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299042	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35720984	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3819398	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712252	0.98[ASN][1000 genomes]
rs4715976	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6912499	1.00[ASN][1000 genomes]
rs6929454	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs727734	1.00[ASN][1000 genomes]
rs760660	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748741	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763809	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370814	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9383058	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9396587	0.90[AMR][1000 genomes];0.97[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	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2299040	EDN1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15435800-15487600	Weak transcription	Colonic Mucosa	Colon
2	chr6:15444600-15477400	Weak transcription	Hela-S3	cervix
3	chr6:15445400-15474000	Weak transcription	NH-A	brain
4	chr6:15446600-15479800	Weak transcription	Gastric	stomach
5	chr6:15448200-15479800	Weak transcription	Pancreas	Pancrea
6	chr6:15452400-15475800	Weak transcription	Aorta	Aorta
7	chr6:15453000-15481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:15455400-15475600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:15455400-15475600	Weak transcription	Esophagus	oesophagus
10	chr6:15457000-15480800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:15458400-15484200	Weak transcription	Small Intestine	intestine
12	chr6:15458800-15474600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:15460800-15480000	Weak transcription	Stomach Mucosa	stomach
14	chr6:15461600-15491000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:15463000-15479800	Weak transcription	Fetal Brain Male	brain
16	chr6:15463200-15476600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:15463600-15473000	Weak transcription	Osteobl	bone
18	chr6:15463600-15473400	Weak transcription	NHEK	skin
19	chr6:15463600-15473600	Weak transcription	NHDF-Ad	bronchial
20	chr6:15463800-15473600	Weak transcription	Right Atrium	heart
21	chr6:15463800-15476400	Weak transcription	Ovary	ovary
22	chr6:15463800-15479800	Weak transcription	Brain Germinal Matrix	brain
23	chr6:15464400-15474000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:15464400-15474000	Strong transcription	Fetal Thymus	thymus
25	chr6:15464400-15474000	Weak transcription	HSMMtube	muscle
26	chr6:15464800-15474000	Weak transcription	Fetal Heart	heart
27	chr6:15464800-15479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:15465600-15480000	Weak transcription	Fetal Brain Female	brain
29	chr6:15466600-15475000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:15467600-15473400	Weak transcription	Brain Substantia Nigra	brain
31	chr6:15468400-15476000	Strong transcription	Primary B cells from cord blood	blood
32	chr6:15468400-15478200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:15468600-15472800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:15468600-15474000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:15468600-15474200	Strong transcription	Thymus	Thymus
36	chr6:15468600-15474400	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr6:15468600-15475600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr6:15468600-15476400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr6:15468600-15476600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:15468600-15476800	Strong transcription	Primary T cells from cord blood	blood
41	chr6:15468800-15473200	Strong transcription	GM12878-XiMat	blood
42	chr6:15468800-15476200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:15468800-15476200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:15468800-15476200	Strong transcription	Dnd41	blood
45	chr6:15468800-15476800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr6:15468800-15477600	Strong transcription	HepG2	liver
47	chr6:15468800-15478400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:15469000-15475600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:15469200-15474600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:15469400-15472800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links