Variant report

Variant	rs1841828
Chromosome Location	chr4:22431406-22431407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22425322..22428021-chr4:22430037..22432573,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10805234	0.94[ASW][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes]
rs10938896	0.90[AFR][1000 genomes]
rs10938897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938898	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938899	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11933055	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11935142	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940612	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102647	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs13109695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13140367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1462995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462996	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1462997	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1564135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564136	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872669	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs1841824	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1841825	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841826	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841827	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126635	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2323521	0.80[MKK][hapmap]
rs2323522	0.89[AFR][1000 genomes]
rs4583743	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs4611916	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4627850	0.87[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59602170	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448156	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6823735	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830873	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831918	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6853811	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854785	0.87[EUR][1000 genomes]
rs6855127	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7670841	0.94[ASW][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes]
rs7688074	0.84[ASN][1000 genomes]
rs964549	0.81[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1841828	LGI2	cis	cerebellum	SCAN
rs1841828	GPR125	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22371600-22449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:22383200-22438000	Weak transcription	Lung	lung
3	chr4:22383600-22442800	Weak transcription	A549	lung
4	chr4:22386000-22446600	Weak transcription	Fetal Thymus	thymus
5	chr4:22388200-22432400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:22388200-22442800	Weak transcription	Brain Germinal Matrix	brain
7	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
9	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
10	chr4:22390600-22439600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:22390600-22456200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:22393000-22435200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:22393400-22444800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:22393800-22446400	Weak transcription	NH-A	brain
17	chr4:22393800-22453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:22399800-22442800	Weak transcription	Fetal Brain Female	brain
19	chr4:22400000-22448000	Weak transcription	Left Ventricle	heart
20	chr4:22400800-22449600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:22400800-22461800	Weak transcription	Gastric	stomach
22	chr4:22405400-22446000	Weak transcription	Pancreas	Pancrea
23	chr4:22412800-22446000	Weak transcription	Thymus	Thymus
24	chr4:22416800-22449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:22417600-22442200	Weak transcription	Hela-S3	cervix
26	chr4:22417800-22436200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:22418000-22435200	Strong transcription	Liver	Liver
28	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
30	chr4:22420200-22436400	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
32	chr4:22420800-22436400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:22421200-22442600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:22422000-22441400	Weak transcription	Right Ventricle	heart
35	chr4:22422000-22453400	Weak transcription	Esophagus	oesophagus
36	chr4:22422600-22442800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:22423800-22432000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr4:22424400-22457800	Weak transcription	Dnd41	blood
39	chr4:22424600-22448000	Weak transcription	Fetal Kidney	kidney
40	chr4:22424800-22432400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:22426200-22436800	Weak transcription	HepG2	liver
43	chr4:22426200-22442400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:22426200-22443200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:22426400-22437400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:22426600-22437000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:22426800-22442800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:22427000-22439000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:22427400-22433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:22427400-22444400	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links