Variant report

Variant	rs1007858
Chromosome Location	chr1:45912005-45912006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45911582..45914439-chr1:45956786..45959560,2	MCF-7	breast:
2	chr1:45909662..45912748-chr1:46049170..46051238,3	K562	blood:
3	chr1:45185686..45188645-chr1:45911904..45916930,4	K562	blood:

Variant related genes	Relation type
ENSG00000070759	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1006216	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10789464	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1084166	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10890327	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890330	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211101	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211108	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211111	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211117	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211118	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211123	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211124	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12029322	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12037201	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037411	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042903	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12046816	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12066142	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067642	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097497	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12410493	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12564806	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1417578	0.85[EUR][1000 genomes]
rs1494812	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17395553	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1771551	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1826691	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2050884	0.85[EUR][1000 genomes]
rs2055145	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088100	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2153607	0.81[EUR][1000 genomes]
rs2153608	0.81[EUR][1000 genomes]
rs2153609	0.82[EUR][1000 genomes]
rs2185549	0.82[EUR][1000 genomes]
rs2298018	0.81[EUR][1000 genomes]
rs2487442	0.87[EUR][1000 genomes]
rs2492836	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2492840	0.85[EUR][1000 genomes]
rs28555082	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3219463	0.81[EUR][1000 genomes]
rs3219472	0.81[EUR][1000 genomes]
rs3790582	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790583	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4633317	0.82[AMR][1000 genomes]
rs4660301	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660849	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660851	0.86[EUR][1000 genomes]
rs4660852	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660853	0.86[EUR][1000 genomes]
rs4660854	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4660855	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4660858	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660863	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5015340	0.82[AMR][1000 genomes]
rs55642258	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788261	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61788262	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61788281	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61788285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788336	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61791362	0.84[EUR][1000 genomes]
rs61791368	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61791369	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67683090	0.82[AMR][1000 genomes]
rs713358	0.82[AMR][1000 genomes]
rs7417107	0.85[EUR][1000 genomes]
rs7528573	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531253	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7532762	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7543428	0.86[EUR][1000 genomes]
rs7544178	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553318	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs781226	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs781230	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs781232	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs884962	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326141	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429072	0.81[EUR][1000 genomes]
rs9429074	0.81[EUR][1000 genomes]
rs9429076	0.82[EUR][1000 genomes]
rs9429158	0.83[EUR][1000 genomes]
rs9429159	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429160	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429161	0.86[EUR][1000 genomes]
rs9729395	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	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
5	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
6	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
7	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
8	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
9	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1007858	TESK2	cis	Whole Blood	GTEx
rs1007858	PRDX1	cis	Thyroid	GTEx
rs1007858	MMACHC	cis	multi-tissue	Pritchard
rs1007858	C2orf49	trans	lymphoblastoid	RTeQTL
rs1007858	MUTYH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45888200-45920600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:45889800-45940600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:45902600-45924200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:45903200-45920600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:45905200-45921000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:45907000-45919600	Weak transcription	Primary T cells from cord blood	blood
7	chr1:45908600-45920600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:45908600-45920600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:45909000-45924600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:45909200-45922400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:45910400-45912400	Weak transcription	Liver	Liver
12	chr1:45910600-45912200	Enhancers	Gastric	stomach
13	chr1:45910600-45920200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:45910800-45912200	Weak transcription	HepG2	liver
15	chr1:45911000-45912600	Weak transcription	Ovary	ovary
16	chr1:45911000-45918200	Weak transcription	Fetal Intestine Small	intestine
17	chr1:45911000-45930400	Weak transcription	Psoas Muscle	Psoas
18	chr1:45911400-45924400	Weak transcription	Placenta	Placenta
19	chr1:45911600-45914800	Enhancers	K562	blood
20	chr1:45911800-45912800	Enhancers	Stomach Mucosa	stomach

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