Variant report

Variant	rs61828624
Chromosome Location	chr1:174286380-174286381
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10127823	0.82[EUR][1000 genomes]
rs12562344	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564848	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564858	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564876	0.80[EUR][1000 genomes]
rs12565675	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566643	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12567854	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12567864	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12568869	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12737218	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1407126	0.85[EUR][1000 genomes]
rs16828467	0.85[EUR][1000 genomes]
rs16846667	0.82[EUR][1000 genomes]
rs16846688	0.85[EUR][1000 genomes]
rs1890881	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2015075	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41265242	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41266044	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4140468	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57651489	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58866024	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60005461	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60039606	0.82[EUR][1000 genomes]
rs61827889	0.85[EUR][1000 genomes]
rs61827901	0.87[EUR][1000 genomes]
rs61827902	0.87[EUR][1000 genomes]
rs61827903	0.87[EUR][1000 genomes]
rs61827904	0.90[EUR][1000 genomes]
rs61827905	0.92[EUR][1000 genomes]
rs61828571	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61828574	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828575	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828576	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828577	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828578	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61828580	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828583	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828584	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828587	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828589	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828590	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828591	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828592	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828595	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828622	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828625	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828627	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61828630	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61828631	0.82[ASN][1000 genomes]
rs61828635	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61828641	0.81[ASN][1000 genomes]
rs61828645	0.80[EUR][1000 genomes]
rs61828653	0.80[EUR][1000 genomes]
rs73036674	0.83[AFR][1000 genomes]
rs7525325	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9970174	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
9	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
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	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
12	nsv872554	chr1:174209978-174291950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	esv1795045	chr1:174273004-174346276	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61828624	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174270800-174289800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:174271000-174286400	Weak transcription	Spleen	Spleen
3	chr1:174273200-174288800	Weak transcription	Small Intestine	intestine
4	chr1:174275600-174287600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:174276200-174289400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:174283600-174286800	ZNF genes & repeats	GM12878-XiMat	blood
7	chr1:174283600-174287200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
8	chr1:174283800-174287600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr1:174284200-174287400	ZNF genes & repeats	Adipose Nuclei	Adipose
10	chr1:174284400-174286600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr1:174284600-174287200	ZNF genes & repeats	Primary B cells from cord blood	blood
12	chr1:174284600-174294600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:174284800-174288600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:174284800-174289000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:174284800-174294400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:174285000-174288600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:174285200-174286400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:174285200-174287200	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr1:174285200-174288400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:174285200-174290200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:174285200-174294800	Weak transcription	Right Ventricle	heart
22	chr1:174285200-174295200	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:174285400-174286400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:174285400-174286400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:174285400-174289400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:174285600-174286400	ZNF genes & repeats	Ovary	ovary
27	chr1:174285600-174287200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr1:174285600-174287200	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr1:174285600-174287200	ZNF genes & repeats	Lung	lung
30	chr1:174285800-174286600	ZNF genes & repeats	Fetal Stomach	stomach
31	chr1:174285800-174286800	Strong transcription	Left Ventricle	heart
32	chr1:174285800-174286800	ZNF genes & repeats	Dnd41	blood
33	chr1:174285800-174287000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:174285800-174287000	ZNF genes & repeats	Aorta	Aorta
35	chr1:174285800-174287200	Strong transcription	Liver	Liver
36	chr1:174285800-174287400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr1:174285800-174288400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:174285800-174290000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:174286000-174287000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:174286000-174287000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:174286000-174287000	ZNF genes & repeats	Pancreas	Pancrea
42	chr1:174286000-174289400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:174286000-174289600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:174286000-174296400	Weak transcription	Brain Angular Gyrus	brain
45	chr1:174286200-174286800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:174286200-174287000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:174286200-174288600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:174286200-174288800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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