Variant report

Variant	rs9425430
Chromosome Location	chr1:173857283-173857284
allele	A/G
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:0)
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	chr1:173639722..173641847-chr1:173856843..173859341,2	K562	blood:
2	chr1:173830453..173832716-chr1:173857010..173859587,2	K562	blood:
3	chr1:173828135..173830893-chr1:173854579..173857617,3	MCF-7	breast:
4	chr1:173854070..173860394-chr1:173860539..173867294,11	MCF-7	breast:
5	chr1:173835275..173839251-chr1:173856381..173859353,4	K562	blood:
6	chr1:173857110..173859005-chr1:173990596..173992280,2	K562	blood:
7	chr1:173856030..173858273-chr1:173864244..173866649,2	K562	blood:
8	chr1:173831191..173840458-chr1:173852193..173864862,18	MCF-7	breast:
9	chr1:173845188..173847906-chr1:173855416..173857290,2	MCF-7	breast:
10	chr1:173853006..173854798-chr1:173856901..173859018,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234741	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000135870	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10798295	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs10798301	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10798302	0.87[CHB][hapmap]
rs12066153	0.87[CHB][hapmap]
rs12071594	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071663	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12078824	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322770	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1322775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322780	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799876	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884994	0.83[CHB][hapmap]
rs1951627	0.87[CHB][hapmap];0.90[GIH][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs2065171	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295366	0.81[MEX][hapmap]
rs4652229	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971204	0.87[YRI][hapmap]
rs5877	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665484	0.87[CHB][hapmap]
rs6677660	0.87[CHB][hapmap]
rs6686083	0.87[CHB][hapmap]
rs6689285	0.87[CHB][hapmap]
rs6696163	0.87[CHB][hapmap]
rs714624	0.87[CHB][hapmap]
rs7349095	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7413166	0.86[CHB][hapmap]
rs7544605	0.85[AMR][1000 genomes]
rs7552939	0.83[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9286895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425435	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425755	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425756	0.81[MEX][hapmap]
rs9425765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425766	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9425430		cis	Lymphoblastoid	GTEx
rs9425430	DARS2	cis	cerebellum	SCAN
rs9425430	SNORD78	cis	parietal	SCAN
rs9425430	PRDX6	cis	parietal	SCAN
rs9425430	FMO1	cis	cerebellum	SCAN
rs9425430	CENPL	cis	lymphoblastoid	seeQTL
rs9425430	RABGAP1L	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
2	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:173839000-173862800	Weak transcription	HMEC	breast
4	chr1:173841000-173864400	Weak transcription	Fetal Heart	heart
5	chr1:173841000-173868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:173842800-173859200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:173853200-173858000	Strong transcription	Fetal Muscle Leg	muscle
8	chr1:173853400-173857800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:173853400-173865200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:173853800-173858600	Strong transcription	Placenta	Placenta
11	chr1:173854000-173857400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:173854000-173858800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:173854000-173858800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr1:173854000-173859400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:173854200-173857600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:173854200-173858200	Strong transcription	Left Ventricle	heart
17	chr1:173854200-173858800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:173854600-173857400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:173854600-173857600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:173854600-173858400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:173854600-173858600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:173854800-173857400	Strong transcription	Brain Cingulate Gyrus	brain
23	chr1:173854800-173857400	Strong transcription	Brain Hippocampus Middle	brain
24	chr1:173854800-173857400	Strong transcription	HepG2	liver
25	chr1:173854800-173857400	Strong transcription	HSMM	muscle
26	chr1:173854800-173857600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr1:173854800-173857600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:173854800-173857800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr1:173854800-173858600	Strong transcription	Liver	Liver
30	chr1:173855000-173857400	Strong transcription	Fetal Intestine Large	intestine
31	chr1:173855000-173857600	Strong transcription	Fetal Kidney	kidney
32	chr1:173855000-173858800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:173855200-173857400	Strong transcription	HSMMtube	muscle
34	chr1:173855200-173857600	Strong transcription	Osteobl	bone
35	chr1:173855400-173858200	Weak transcription	Colonic Mucosa	Colon
36	chr1:173855400-173863000	Weak transcription	NHEK	skin
37	chr1:173855400-173868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:173855600-173866800	Weak transcription	Pancreas	Pancrea
39	chr1:173855600-173875400	Weak transcription	NH-A	brain
40	chr1:173855800-173857800	Genic enhancers	Primary T cells from cord blood	blood
41	chr1:173855800-173858600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:173855800-173858800	Weak transcription	A549	lung
43	chr1:173855800-173859400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:173855800-173860200	Weak transcription	Spleen	Spleen
45	chr1:173855800-173863400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:173855800-173873000	Weak transcription	Fetal Intestine Small	intestine
47	chr1:173855800-173880400	Weak transcription	Thymus	Thymus
48	chr1:173856000-173857600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:173856000-173857800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr1:173856000-173858000	Weak transcription	Brain Substantia Nigra	brain

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