Variant report

Variant	rs1419305
Chromosome Location	chr1:223912748-223912749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223898332..223906168-chr1:223910455..223917097,17	K562	blood:
2	chr1:223907382..223910369-chr1:223910890..223914136,6	MCF-7	breast:
3	chr1:223889048..223892009-chr1:223912186..223915983,3	K562	blood:
4	chr1:223882722..223885299-chr1:223910440..223912763,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10799550	0.84[EUR][1000 genomes]
rs10916600	0.95[EUR][1000 genomes]
rs10916601	0.94[EUR][1000 genomes]
rs10916602	0.94[EUR][1000 genomes]
rs10916603	0.95[EUR][1000 genomes]
rs10916634	1.00[CEU][hapmap];0.96[GIH][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10916646	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11580460	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588475	0.92[ASN][1000 genomes]
rs12066704	0.87[CEU][hapmap]
rs12069561	0.87[CEU][hapmap]
rs12070364	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074091	0.94[EUR][1000 genomes]
rs1222138	0.87[CEU][hapmap]
rs1222141	0.87[CEU][hapmap]
rs12568612	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs1539707	0.93[EUR][1000 genomes]
rs17556570	0.87[CEU][hapmap]
rs17598	0.87[CEU][hapmap]
rs1779658	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1892076	0.95[EUR][1000 genomes]
rs1892077	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2186006	1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs28370014	0.93[EUR][1000 genomes]
rs28739569	0.92[EUR][1000 genomes]
rs3738373	0.87[CEU][hapmap]
rs3738374	0.87[CEU][hapmap]
rs4511081	0.83[EUR][1000 genomes]
rs4653499	0.94[EUR][1000 genomes]
rs4653500	0.95[EUR][1000 genomes]
rs4653522	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs61823962	0.80[EUR][1000 genomes]
rs61823965	0.83[EUR][1000 genomes]
rs61823966	0.94[EUR][1000 genomes]
rs61823967	0.94[EUR][1000 genomes]
rs61823968	0.94[EUR][1000 genomes]
rs61823980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669046	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6669080	0.82[CEU][hapmap]
rs6674733	0.96[EUR][1000 genomes]
rs6702314	0.82[EUR][1000 genomes]
rs6702430	0.81[EUR][1000 genomes]
rs6703104	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs7412088	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7414311	0.94[EUR][1000 genomes]
rs751609	0.86[CEU][hapmap]
rs7517684	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7525446	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7543197	1.00[CEU][hapmap]
rs7547642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7555491	1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1419305	MARK1	cis	parietal	SCAN
rs1419305	CAPN2	Cis_1M	lymphoblastoid	RTeQTL
rs1419305	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:223904400-223913000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:223904400-223922400	Genic enhancers	NHLF	lung
7	chr1:223904600-223913600	Strong transcription	Brain Anterior Caudate	brain
8	chr1:223904600-223914000	Genic enhancers	NHDF-Ad	bronchial
9	chr1:223904800-223913200	Strong transcription	Fetal Stomach	stomach
10	chr1:223904800-223914000	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr1:223906000-223913800	Weak transcription	Primary B cells from cord blood	blood
12	chr1:223906200-223913000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr1:223906200-223915600	Weak transcription	Aorta	Aorta
14	chr1:223906400-223913600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:223906400-223913600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:223906600-223913800	Weak transcription	Fetal Thymus	thymus
17	chr1:223906600-223921000	Weak transcription	Fetal Brain Male	brain
18	chr1:223907400-223913200	Weak transcription	K562	blood
19	chr1:223907600-223913400	Genic enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:223907800-223913200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr1:223907800-223913600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:223907800-223913600	Weak transcription	Fetal Heart	heart
23	chr1:223907800-223913800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:223908400-223913600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:223908800-223913400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:223908800-223913600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:223909000-223914000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:223909200-223913400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:223909200-223913400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:223909200-223913400	Weak transcription	Right Atrium	heart
31	chr1:223909200-223913600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:223909200-223913800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:223909200-223914000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:223909400-223913000	Strong transcription	HMEC	breast
35	chr1:223909400-223913400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:223909400-223913400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:223909400-223913600	Weak transcription	Brain Substantia Nigra	brain
38	chr1:223909400-223913600	Weak transcription	Psoas Muscle	Psoas
39	chr1:223909400-223913800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:223909400-223913800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:223909400-223914000	Weak transcription	Liver	Liver
42	chr1:223909400-223914000	Weak transcription	Brain Germinal Matrix	brain
43	chr1:223909600-223913600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:223909600-223913600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:223909600-223913600	Weak transcription	Ovary	ovary
46	chr1:223909600-223913800	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:223909600-223914000	Weak transcription	Fetal Brain Female	brain
48	chr1:223909800-223913400	Genic enhancers	A549	lung
49	chr1:223909800-223913800	Strong transcription	Fetal Intestine Small	intestine
50	chr1:223909800-223914200	Weak transcription	Fetal Kidney	kidney

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