Variant report

Variant	rs6425423
Chromosome Location	chr1:171772865-171772866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171771604..171774137-chr1:171780038..171783681,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252134	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10489253	0.84[YRI][hapmap]
rs10798636	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs10798667	0.94[ASN][1000 genomes]
rs10913644	0.84[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11587288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590059	0.85[AFR][1000 genomes]
rs11803889	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs12022693	0.85[AFR][1000 genomes]
rs12034454	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039034	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12566700	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs16843385	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17597528	0.85[AFR][1000 genomes]
rs2206541	0.84[YRI][hapmap]
rs2232812	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2232816	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232818	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232826	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294717	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753538	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56167663	0.85[AFR][1000 genomes]
rs56178029	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57476157	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59302445	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60502293	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60956160	0.87[EUR][1000 genomes]
rs6425428	0.85[AFR][1000 genomes]
rs6425438	0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6425439	0.92[ASN][1000 genomes]
rs6684594	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6690544	0.83[YRI][hapmap]
rs6691222	0.91[CHB][hapmap];0.96[JPT][hapmap];0.87[ASN][1000 genomes]
rs6695502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6700184	0.87[YRI][hapmap]
rs72703115	0.94[ASN][1000 genomes]
rs7537770	0.86[YRI][hapmap]
rs7541192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7543608	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7548462	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556602	0.86[YRI][hapmap]
rs7860	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs909958	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs941942	0.84[CEU][hapmap];0.86[EUR][1000 genomes]

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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425423	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:171765000-171774600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:171766000-171774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:171766200-171774400	Weak transcription	Brain Substantia Nigra	brain
5	chr1:171766200-171774600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:171766200-171774600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:171766200-171775400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:171766200-171777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:171766400-171777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:171766600-171774600	Weak transcription	Ovary	ovary
11	chr1:171766600-171774800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:171766600-171774800	Weak transcription	Placenta	Placenta
13	chr1:171766600-171774800	Weak transcription	HepG2	liver
14	chr1:171766800-171774600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:171766800-171774600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:171767000-171774600	Weak transcription	K562	blood
17	chr1:171767000-171774800	Weak transcription	Osteobl	bone
18	chr1:171767000-171777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:171767000-171778600	Weak transcription	NHEK	skin
20	chr1:171767200-171774600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:171767200-171774800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:171767200-171774800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:171767200-171777600	Weak transcription	HMEC	breast
24	chr1:171767400-171773600	Weak transcription	HUVEC	blood vessel
25	chr1:171767400-171774600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:171767400-171774800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:171767400-171774800	Weak transcription	Psoas Muscle	Psoas
28	chr1:171767400-171775000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:171767400-171777200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:171767600-171774800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:171767600-171774800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:171767600-171775000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:171767800-171774600	Weak transcription	GM12878-XiMat	blood
34	chr1:171767800-171774800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:171767800-171774800	Weak transcription	Aorta	Aorta
36	chr1:171767800-171778800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:171767800-171781800	Weak transcription	Thymus	Thymus
38	chr1:171768000-171773000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:171768000-171774600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:171768000-171774800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:171768000-171776600	Weak transcription	Esophagus	oesophagus
42	chr1:171768000-171778600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:171768200-171774800	Weak transcription	Spleen	Spleen
44	chr1:171768200-171774800	Weak transcription	HSMM	muscle
45	chr1:171768400-171775000	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:171768400-171785600	Weak transcription	Gastric	stomach
47	chr1:171769000-171773400	Weak transcription	Fetal Lung	lung
48	chr1:171769400-171773000	Enhancers	NHDF-Ad	bronchial
49	chr1:171769600-171774200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:171769600-171774400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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