Variant report

Variant	rs61827901
Chromosome Location	chr1:174130186-174130187
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:174127459-174131155	GM18505	blood:	n/a	n/a
2	NR2F2	chr1:174127559-174130282	K562	blood:	n/a	n/a
3	MXI1	chr1:174127701-174130263	K562	blood:	n/a	n/a
4	NFATC1	chr1:174129606-174130348	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174129282..174131364-chr1:174167925..174169764,2	K562	blood:
2	chr1:173990484..173993026-chr1:174127463..174130354,3	K562	blood:
3	chr1:173990191..173994093-chr1:174126470..174130234,3	MCF-7	breast:
4	chr1:174128312..174130705-chr1:174967510..174969928,2	K562	blood:
5	chr1:173835391..173837802-chr1:174127164..174130207,3	MCF-7	breast:
6	chr1:173445824..173447952-chr1:174128991..174131620,2	K562	blood:
7	chr1:173835729..173840438-chr1:174127915..174131019,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000227373	TF binding region
ENSG00000185278	Chromatin interaction
ENSG00000238872	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000117592	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10127823	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10494491	0.82[EUR][1000 genomes]
rs12562344	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12562959	0.82[EUR][1000 genomes]
rs12564848	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12564858	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12564876	1.00[AFR][1000 genomes]
rs12565675	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12565973	0.82[EUR][1000 genomes]
rs12566022	0.82[EUR][1000 genomes]
rs12566642	0.82[EUR][1000 genomes]
rs12566643	0.95[EUR][1000 genomes]
rs12566842	0.82[EUR][1000 genomes]
rs12567854	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12567864	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12568869	1.00[AFR][1000 genomes]
rs12737218	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1321637	0.82[EUR][1000 genomes]
rs1407126	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16828467	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846667	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16846688	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1890881	0.95[EUR][1000 genomes]
rs2015075	1.00[AFR][1000 genomes];0.95[EUR][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];0.94[EUR][1000 genomes]
rs41266044	0.95[EUR][1000 genomes]
rs4140468	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56926540	0.82[EUR][1000 genomes]
rs57651489	0.87[EUR][1000 genomes]
rs58866024	0.90[EUR][1000 genomes]
rs60005461	0.90[EUR][1000 genomes]
rs60039606	0.95[EUR][1000 genomes];0.92[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]
rs61827889	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827900	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61828571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61828574	0.92[EUR][1000 genomes]
rs61828575	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828576	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828577	0.95[EUR][1000 genomes]
rs61828578	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828580	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828583	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828584	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828587	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828589	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828590	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828591	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828592	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828595	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61828622	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61828624	0.87[EUR][1000 genomes]
rs61828625	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61828627	1.00[AFR][1000 genomes];0.85[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]
rs61828895	0.82[EUR][1000 genomes]
rs61828898	0.82[EUR][1000 genomes]
rs61828899	0.82[EUR][1000 genomes]
rs6684527	0.82[EUR][1000 genomes]
rs7525325	0.94[EUR][1000 genomes]
rs9425779	0.82[EUR][1000 genomes]
rs965498	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61827901	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174127600-174130200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:174127800-174130200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:174128000-174130200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:174128000-174130200	Active TSS	Fetal Heart	heart
5	chr1:174128000-174130200	Active TSS	Fetal Intestine Small	intestine
6	chr1:174128000-174131400	Active TSS	GM12878-XiMat	blood
7	chr1:174128000-174131600	Active TSS	Duodenum Mucosa	Duodenum
8	chr1:174128200-174130200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:174128200-174130200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:174129000-174132600	Active TSS	Right Atrium	heart
11	chr1:174129200-174130200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr1:174129200-174130200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr1:174129200-174130200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:174129400-174130200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:174129400-174130200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr1:174129400-174130200	Flanking Active TSS	K562	blood
17	chr1:174129600-174130200	Flanking Active TSS	Hela-S3	cervix
18	chr1:174129600-174131000	Weak transcription	Esophagus	oesophagus
19	chr1:174129600-174131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:174129600-174132600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:174129600-174134000	Weak transcription	Stomach Mucosa	stomach
22	chr1:174129600-174164800	Weak transcription	Gastric	stomach
23	chr1:174129600-174173200	Weak transcription	Pancreas	Pancrea
24	chr1:174129800-174130200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:174129800-174130200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:174129800-174130200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:174129800-174130200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:174129800-174130200	Enhancers	Colon Smooth Muscle	Colon
29	chr1:174129800-174130200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr1:174129800-174130200	Enhancers	Fetal Stomach	stomach
31	chr1:174129800-174130200	Weak transcription	Left Ventricle	heart
32	chr1:174129800-174130200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:174129800-174130200	Flanking Active TSS	HepG2	liver
34	chr1:174129800-174130400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:174129800-174130600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:174129800-174130800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:174129800-174131000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:174129800-174131000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:174129800-174131000	Weak transcription	Psoas Muscle	Psoas
40	chr1:174129800-174131200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:174129800-174131400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:174129800-174131400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:174129800-174131800	Enhancers	Primary B cells from peripheral blood	blood
44	chr1:174129800-174131800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr1:174129800-174133200	Weak transcription	Small Intestine	intestine
46	chr1:174129800-174134800	Weak transcription	Ovary	ovary
47	chr1:174129800-174135000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:174129800-174135000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:174129800-174135000	Weak transcription	Spleen	Spleen
50	chr1:174129800-174137000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links