Variant report

Variant	rs61828571
Chromosome Location	chr1:174158831-174158832
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174127315..174129542-chr1:174157922..174159805,2	K562	blood:
2	chr1:174157753..174160187-chr1:174164644..174167517,2	MCF-7	breast:
3	chr1:174128241..174130281-chr1:174157762..174160299,2	K562	blood:

Variant related genes	Relation type
ENSG00000227373	Chromatin interaction
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10127823	0.89[EUR][1000 genomes]
rs10494491	0.82[EUR][1000 genomes]
rs12562344	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12562959	0.82[EUR][1000 genomes]
rs12564848	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564858	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12564876	1.00[AFR][1000 genomes]
rs12565675	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12565973	0.82[EUR][1000 genomes]
rs12566022	0.82[EUR][1000 genomes]
rs12566642	0.82[EUR][1000 genomes]
rs12566643	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12566842	0.82[EUR][1000 genomes]
rs12567854	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12567864	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12568869	1.00[AFR][1000 genomes]
rs12737218	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1321637	0.82[EUR][1000 genomes]
rs1407126	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16828467	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16846667	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16846688	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1890881	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015075	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2025241	0.82[EUR][1000 genomes]
rs28595073	0.82[EUR][1000 genomes]
rs36013663	0.82[EUR][1000 genomes]
rs41265242	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41266044	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4140468	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56926540	0.82[EUR][1000 genomes]
rs57651489	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58866024	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60005461	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60039606	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826771	0.82[EUR][1000 genomes]
rs61826777	0.81[EUR][1000 genomes]
rs61826779	0.82[EUR][1000 genomes]
rs61826780	0.81[EUR][1000 genomes]
rs61826784	0.81[EUR][1000 genomes]
rs61826824	0.82[EUR][1000 genomes]
rs61826826	0.81[EUR][1000 genomes]
rs61826829	0.84[EUR][1000 genomes]
rs61826831	0.84[EUR][1000 genomes]
rs61826863	1.00[AFR][1000 genomes]
rs61826865	1.00[AFR][1000 genomes]
rs61826867	1.00[AFR][1000 genomes]
rs61826868	1.00[AFR][1000 genomes]
rs61826869	1.00[AFR][1000 genomes]
rs61827889	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61827900	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61828574	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828575	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828576	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828577	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828578	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828580	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828583	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828584	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828587	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828589	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828590	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828591	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828592	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828595	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828622	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61828624	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61828625	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828627	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs61828630	1.00[AFR][1000 genomes]
rs61828631	1.00[AFR][1000 genomes]
rs61828635	1.00[AFR][1000 genomes]
rs61828645	1.00[AFR][1000 genomes]
rs61828653	1.00[AFR][1000 genomes]
rs61828898	0.82[EUR][1000 genomes]
rs61828899	0.82[EUR][1000 genomes]
rs6684527	0.82[EUR][1000 genomes]
rs7525325	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs965498	0.84[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	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv946458	chr1:174149182-174160829	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61828571	SERPINC1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174129600-174164800	Weak transcription	Gastric	stomach
2	chr1:174129600-174173200	Weak transcription	Pancreas	Pancrea
3	chr1:174134800-174159800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:174136400-174160000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:174138400-174160000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:174139000-174159800	Weak transcription	Right Atrium	heart
7	chr1:174144000-174178200	Weak transcription	Left Ventricle	heart
8	chr1:174148800-174159600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:174151800-174159600	Weak transcription	K562	blood
10	chr1:174154200-174173600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:174158200-174159800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:174158600-174160000	Enhancers	GM12878-XiMat	blood
13	chr1:174158800-174159000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:174158800-174159400	Weak transcription	Small Intestine	intestine
15	chr1:174158800-174159600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:174158800-174159800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:174158800-174160200	Enhancers	Primary T cells fromperipheralblood	blood

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