Variant report

Variant	rs1417578
Chromosome Location	chr1:45850590-45850591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45843258..45845570-chr1:45849116..45850703,2	K562	blood:
2	chr1:45849151..45851043-chr1:45857348..45859085,2	K562	blood:
3	chr1:45849602..45851336-chr1:45956467..45958174,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070759	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1006216	0.87[EUR][1000 genomes]
rs1007858	0.85[EUR][1000 genomes]
rs1084166	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10890327	0.89[EUR][1000 genomes]
rs10890330	0.80[EUR][1000 genomes]
rs11211101	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211108	0.91[EUR][1000 genomes]
rs11211111	0.86[EUR][1000 genomes]
rs11211117	0.87[EUR][1000 genomes]
rs11211118	0.87[EUR][1000 genomes]
rs12037201	0.87[EUR][1000 genomes]
rs12037411	0.96[EUR][1000 genomes]
rs12046816	0.90[EUR][1000 genomes]
rs12067642	0.80[EUR][1000 genomes]
rs12097497	0.89[EUR][1000 genomes]
rs12139364	0.87[JPT][hapmap]
rs12410493	0.88[EUR][1000 genomes]
rs1494812	0.89[EUR][1000 genomes]
rs1538969	0.86[EUR][1000 genomes]
rs1538970	0.88[EUR][1000 genomes]
rs17395553	0.96[EUR][1000 genomes]
rs1771551	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1826691	0.90[EUR][1000 genomes]
rs2050884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055145	0.80[EUR][1000 genomes]
rs2088100	0.89[EUR][1000 genomes]
rs2153607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153609	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2185549	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2298018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2487442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492836	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2492840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555082	0.87[EUR][1000 genomes]
rs3219463	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3219472	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3219489	0.82[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3790582	0.90[EUR][1000 genomes]
rs4520450	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4660301	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660849	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4660851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660852	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660853	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4660854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4660855	0.88[EUR][1000 genomes]
rs4660858	0.87[EUR][1000 genomes]
rs55642258	0.80[EUR][1000 genomes]
rs61788261	0.89[EUR][1000 genomes]
rs61788262	0.84[EUR][1000 genomes]
rs61788281	0.87[EUR][1000 genomes]
rs61788285	0.80[EUR][1000 genomes]
rs61791362	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61791368	0.87[EUR][1000 genomes]
rs61791369	0.91[EUR][1000 genomes]
rs6670303	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72686460	0.86[EUR][1000 genomes]
rs7417107	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525849	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7528573	0.87[EUR][1000 genomes]
rs7531253	0.91[EUR][1000 genomes]
rs7532762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536135	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7543428	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544178	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7553318	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs781226	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs781230	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs781232	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs884962	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9326141	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9429073	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9429074	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9429076	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9429158	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9429159	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9429160	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429161	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1417578	MMACHC	cis	multi-tissue	Pritchard
rs1417578	TESK2	cis	Whole Blood	GTEx
rs1417578	MUTYH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45826200-45867200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:45827000-45859000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:45839600-45850600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:45839800-45851800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:45840000-45858600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:45841200-45857400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:45841400-45889200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:45842200-45859000	Weak transcription	Right Atrium	heart
9	chr1:45842400-45852400	Weak transcription	Aorta	Aorta
10	chr1:45844200-45858400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:45847400-45853200	Weak transcription	HepG2	liver
12	chr1:45848000-45854000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:45849800-45851800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr1:45850200-45857200	Weak transcription	Fetal Lung	lung
15	chr1:45850400-45851200	Strong transcription	Brain Angular Gyrus	brain
16	chr1:45850400-45851600	Strong transcription	Primary B cells from cord blood	blood

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