Variant report

Variant	rs61827903
Chromosome Location	chr1:174130616-174130617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:174130431-174130723	GM12878	blood:	n/a	n/a
2	RUNX3	chr1:174130251-174131149	GM12878	blood:	n/a	n/a
3	BHLHE40	chr1:174130576-174131024	GM12878	blood:	n/a	n/a
4	PAX5	chr1:174130381-174130724	GM12878	blood:	n/a	chr1:174130532-174130551
5	POLR2A	chr1:174127459-174131155	GM18505	blood:	n/a	n/a
6	POLR2A	chr1:174130293-174131271	GM12892	blood:	n/a	n/a
7	MAFK	chr1:174130566-174130766	K562	blood:	n/a	n/a
8	PAX5	chr1:174130382-174130771	GM12892	blood:	n/a	chr1:174130532-174130551
9	PAX5	chr1:174130411-174130688	GM12892	blood:	n/a	chr1:174130532-174130551
10	PAX5	chr1:174130346-174130686	GM12878	blood:	n/a	chr1:174130532-174130551
11	POLR2A	chr1:174130351-174130678	GM12878	blood:	n/a	n/a
12	RUNX3	chr1:174130357-174131038	GM12878	blood:	n/a	n/a
13	PAX5	chr1:174130379-174131176	GM12878	blood:	n/a	chr1:174130532-174130551
14	PAX5	chr1:174130434-174130671	GM12878	blood:	n/a	chr1:174130532-174130551
15	UBTF	chr1:174130514-174131050	K562	blood:	n/a	n/a
16	POLR2A	chr1:174130399-174130748	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:174130228-174130843	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:174129282..174131364-chr1:174167925..174169764,2	K562	blood:
2	chr1:174126500..174130155-chr1:174130504..174133704,4	MCF-7	breast:
3	chr1:174128312..174130705-chr1:174967510..174969928,2	K562	blood:
4	chr1:173445824..173447952-chr1:174128991..174131620,2	K562	blood:
5	chr1:173835729..173840438-chr1:174127915..174131019,7	K562	blood:

Variant related genes	Relation type
ENSG00000227373	TF binding region
ENSG00000227373	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000238872	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000152061	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]
rs61827901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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
rs61827903	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174128000-174131400	Active TSS	GM12878-XiMat	blood
2	chr1:174128000-174131600	Active TSS	Duodenum Mucosa	Duodenum
3	chr1:174129000-174132600	Active TSS	Right Atrium	heart
4	chr1:174129600-174131000	Weak transcription	Esophagus	oesophagus
5	chr1:174129600-174131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:174129600-174132600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:174129600-174134000	Weak transcription	Stomach Mucosa	stomach
8	chr1:174129600-174164800	Weak transcription	Gastric	stomach
9	chr1:174129600-174173200	Weak transcription	Pancreas	Pancrea
10	chr1:174129800-174130800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:174129800-174131000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:174129800-174131000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:174129800-174131000	Weak transcription	Psoas Muscle	Psoas
14	chr1:174129800-174131200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:174129800-174131400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:174129800-174131400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:174129800-174131800	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:174129800-174131800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:174129800-174133200	Weak transcription	Small Intestine	intestine
20	chr1:174129800-174134800	Weak transcription	Ovary	ovary
21	chr1:174129800-174135000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:174129800-174135000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:174129800-174135000	Weak transcription	Spleen	Spleen
24	chr1:174129800-174137000	Weak transcription	Fetal Lung	lung
25	chr1:174129800-174145600	Weak transcription	Fetal Thymus	thymus
26	chr1:174129800-174147000	Weak transcription	Fetal Brain Male	brain
27	chr1:174129800-174149600	Weak transcription	Aorta	Aorta
28	chr1:174130000-174130800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr1:174130000-174130800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:174130000-174130800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:174130000-174130800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:174130000-174130800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:174130000-174131200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr1:174130000-174131400	Weak transcription	Brain Angular Gyrus	brain
35	chr1:174130000-174131400	Weak transcription	Thymus	Thymus
36	chr1:174130000-174131600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:174130000-174131800	Enhancers	Dnd41	blood
38	chr1:174130000-174132000	Enhancers	Primary T cells fromperipheralblood	blood
39	chr1:174130000-174132000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:174130000-174133200	Weak transcription	Colonic Mucosa	Colon
41	chr1:174130000-174133200	Weak transcription	Fetal Intestine Large	intestine
42	chr1:174130000-174133200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:174130000-174133600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:174130000-174134800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:174130000-174134800	Weak transcription	Adipose Nuclei	Adipose
46	chr1:174130000-174134800	Weak transcription	Liver	Liver
47	chr1:174130000-174134800	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:174130000-174135400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:174130000-174135400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:174130000-174135800	Weak transcription	Right Ventricle	heart

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