Variant report

Variant	rs61788356
Chromosome Location	chr1:46006675-46006676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45998915..46004761-chr1:46006522..46011880,8	K562	blood:
2	chr1:46006129..46009713-chr1:46009736..46013035,4	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10789464	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10890330	0.81[EUR][1000 genomes]
rs11211123	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11211124	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211128	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211137	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211139	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12029322	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12042903	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12049503	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12066142	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12067642	0.81[EUR][1000 genomes]
rs12077621	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2055145	0.81[EUR][1000 genomes]
rs2883968	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34673142	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34768551	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3790583	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4633317	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660863	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5015340	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55642258	0.81[EUR][1000 genomes]
rs61788285	0.81[EUR][1000 genomes]
rs61788336	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67683090	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs713358	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs868351	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9727262	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9729395	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[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	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
3	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
4	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
5	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
6	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
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs61788356	MMACHC	cis	multi-tissue	Pritchard
rs61788356	TESK2	cis	Whole Blood	GTEx
rs61788356	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs61788356	C2orf49	trans	lymphoblastoid	RTeQTL
rs61788356	PRDX1	cis	Thyroid	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46000800-46016000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:46002600-46009600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:46003000-46007400	Weak transcription	Liver	Liver
4	chr1:46003200-46006800	Weak transcription	Fetal Intestine Small	intestine
5	chr1:46003200-46008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:46003400-46007400	Weak transcription	HepG2	liver
7	chr1:46003400-46007400	Weak transcription	K562	blood
8	chr1:46003400-46007600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:46003600-46007600	Weak transcription	Fetal Intestine Large	intestine
10	chr1:46005400-46008200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:46006200-46009200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:46006400-46006800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:46006400-46007600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr1:46006400-46009400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:46006400-46009400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:46006400-46012200	Enhancers	Primary B cells from peripheral blood	blood
17	chr1:46006600-46009200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links