Variant report

Variant	rs6428143
Chromosome Location	chr1:192947351-192947352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:192919620..192921287-chr1:192946637..192948613,2	K562	blood:
2	chr1:192945670..192948268-chr1:192951433..192953649,3	K562	blood:
3	chr1:192944889..192949055-chr1:192952758..192955789,3	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10801165	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10921296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10921298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10921299	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10921300	0.83[EUR][1000 genomes]
rs11507871	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11507872	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117621	0.83[EUR][1000 genomes]
rs12125252	0.83[EUR][1000 genomes]
rs12125347	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12143913	0.83[EUR][1000 genomes]
rs12531	1.00[CHD][hapmap]
rs1339591	0.91[AMR][1000 genomes]
rs1339593	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1615218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1769054	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1770915	1.00[CHD][hapmap]
rs1775687	1.00[CHD][hapmap]
rs2066216	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2486496	0.91[AMR][1000 genomes]
rs28461227	0.89[EUR][1000 genomes]
rs35686688	0.89[AMR][1000 genomes]
rs6700102	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6700111	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6701258	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs710140	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs710141	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72738572	0.83[EUR][1000 genomes]
rs72738574	0.83[EUR][1000 genomes]
rs72738576	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72738577	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72738582	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7512163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7512241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7513985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7523033	1.00[CHD][hapmap]
rs7547423	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs842792	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs842793	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs842794	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs842798	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs842802	0.91[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs842803	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs842805	0.85[LWK][hapmap];0.90[MEX][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes]
rs842812	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs842815	0.91[AMR][1000 genomes]
rs844528	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9427824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9427825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs946557	0.91[AMR][1000 genomes];0.90[EUR][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	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999499	chr1:192909529-192998421	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv535252	chr1:192909529-192998421	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2762039	chr1:192944821-192949840	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6428143	GLRX2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192937000-192963400	Weak transcription	Aorta	Aorta
2	chr1:192938000-192972800	Weak transcription	Psoas Muscle	Psoas
3	chr1:192940600-192947600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:192944000-192948600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:192944000-192949800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:192944000-192951400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:192944000-192961800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:192944000-192962800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:192944000-192963000	Weak transcription	Pancreas	Pancrea
10	chr1:192944200-192963200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:192944400-192949600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:192944400-192962800	Weak transcription	Osteobl	bone
13	chr1:192945800-192947400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:192945800-192948200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr1:192946200-192947600	Flanking Active TSS	K562	blood
16	chr1:192946400-192947400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:192946400-192947400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:192946400-192947800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:192946400-192948400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:192946600-192947600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:192946800-192947400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:192947000-192947400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:192947000-192968800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:192947200-192948400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links