Variant report

Variant	rs61828653
Chromosome Location	chr1:174352864-174352865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173991563..173993480-chr1:174352055..174354802,2	K562	blood:

Variant related genes	Relation type
ENSG00000224977	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10157872	0.88[ASN][1000 genomes]
rs12562344	0.87[AFR][1000 genomes]
rs12564848	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12564858	1.00[AFR][1000 genomes]
rs12564876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564992	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12565430	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12565675	1.00[AFR][1000 genomes]
rs12567854	1.00[AFR][1000 genomes]
rs12567864	1.00[AFR][1000 genomes]
rs12568182	0.84[ASN][1000 genomes]
rs12568869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12737218	0.87[AFR][1000 genomes]
rs1964103	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2015075	1.00[AFR][1000 genomes]
rs2072758	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35216639	0.85[ASN][1000 genomes]
rs41265242	1.00[AFR][1000 genomes]
rs4140468	1.00[AFR][1000 genomes]
rs56674178	0.88[ASN][1000 genomes]
rs57651489	0.80[EUR][1000 genomes]
rs61439796	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826863	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61826865	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826867	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61826868	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826869	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826873	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826876	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826877	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826879	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826881	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826882	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826883	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61826887	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826888	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826902	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61826903	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61826904	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61826909	0.85[ASN][1000 genomes]
rs61827900	1.00[AFR][1000 genomes]
rs61827901	1.00[AFR][1000 genomes]
rs61827902	1.00[AFR][1000 genomes]
rs61827903	1.00[AFR][1000 genomes]
rs61827904	1.00[AFR][1000 genomes]
rs61827905	1.00[AFR][1000 genomes]
rs61828571	1.00[AFR][1000 genomes]
rs61828575	1.00[AFR][1000 genomes]
rs61828576	1.00[AFR][1000 genomes]
rs61828578	1.00[AFR][1000 genomes]
rs61828580	1.00[AFR][1000 genomes]
rs61828583	1.00[AFR][1000 genomes]
rs61828584	1.00[AFR][1000 genomes]
rs61828587	1.00[AFR][1000 genomes]
rs61828589	1.00[AFR][1000 genomes]
rs61828590	1.00[AFR][1000 genomes]
rs61828591	1.00[AFR][1000 genomes]
rs61828592	1.00[AFR][1000 genomes]
rs61828595	1.00[AFR][1000 genomes]
rs61828622	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61828624	0.80[EUR][1000 genomes]
rs61828625	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61828627	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61828630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61828631	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61828641	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828652	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61828654	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9970174	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	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
4	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
5	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
6	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
7	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv872555	chr1:174343705-174565720	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61828653	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174298000-174361800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:174310600-174362400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:174315600-174366400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:174318800-174369800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:174319200-174362600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:174322400-174363000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:174325800-174382800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:174327400-174362000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:174327600-174362200	Weak transcription	Aorta	Aorta
10	chr1:174328800-174366400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:174334800-174361800	Weak transcription	Left Ventricle	heart
12	chr1:174335000-174361800	Weak transcription	Primary B cells from cord blood	blood
13	chr1:174341200-174353400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:174341800-174372200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:174343000-174362200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:174344000-174362200	Weak transcription	GM12878-XiMat	blood
17	chr1:174346800-174362200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:174351000-174369000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:174352000-174366000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:174352200-174366400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:174352400-174353000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr1:174352600-174353000	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:174352600-174353200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:174352600-174353200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr1:174352600-174362800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links