Variant report

Variant	rs12086019
Chromosome Location	chr1:173911909-173911910
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173808363..173810424-chr1:173909776..173912123,2	MCF-7	breast:
2	chr1:173833863..173839457-chr1:173910408..173918981,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10127823	0.83[EUR][1000 genomes]
rs10494491	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10912702	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912710	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912716	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912717	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912721	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11489771	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12029025	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12058585	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12060191	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12060331	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12060401	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12063266	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12063818	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12067580	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12069129	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12071784	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12072602	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12072905	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12077782	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12077812	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12083593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12085939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12086826	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12087212	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12089005	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12089405	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093885	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12562588	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12562959	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12563156	0.87[EUR][1000 genomes]
rs12565352	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565973	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12566022	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566642	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12566651	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566842	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1321637	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1322776	0.80[EUR][1000 genomes]
rs1322778	0.81[EUR][1000 genomes]
rs1322779	0.85[EUR][1000 genomes]
rs13375205	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1407596	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1407597	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16846641	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16846667	0.83[EUR][1000 genomes]
rs1987871	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1987873	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2009083	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2025241	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2227588	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2227590	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2227593	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2227594	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2227595	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2227596	0.80[ASN][1000 genomes]
rs2227597	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2227601	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2227612	0.85[EUR][1000 genomes]
rs2295958	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28595073	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2860841	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2860845	0.93[EUR][1000 genomes]
rs2901784	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36013663	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3980286	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4536054	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652283	0.83[EUR][1000 genomes]
rs4652298	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4652328	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56926540	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57849055	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57995528	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58092103	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59520434	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59960208	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60265316	0.84[EUR][1000 genomes]
rs60551050	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826771	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826774	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826777	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826779	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826780	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61826784	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826785	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61826823	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61826824	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61826826	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61826829	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61826831	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61827928	0.81[EUR][1000 genomes]
rs61827930	0.81[EUR][1000 genomes]
rs61827932	0.81[EUR][1000 genomes]
rs61827933	0.81[EUR][1000 genomes]
rs61827934	0.84[EUR][1000 genomes]
rs61827935	0.81[EUR][1000 genomes]
rs61827936	0.85[EUR][1000 genomes]
rs61827938	0.88[EUR][1000 genomes]
rs61827956	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61827957	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61827959	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61828895	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61828898	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61828899	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61828900	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61828901	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425262	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425264	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425266	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425267	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425271	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425272	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6657380	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6661182	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6665720	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6665880	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668543	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6676307	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6680088	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6683276	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6684527	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6688176	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6695887	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695940	0.92[EUR][1000 genomes]
rs6698123	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702454	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703547	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677	0.84[EUR][1000 genomes]
rs724416	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73039035	0.87[EUR][1000 genomes]
rs7523504	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528380	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530661	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7547880	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7549291	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs767053	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9283385	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9286896	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425431	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9425433	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9425434	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9425436	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9425762	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9425772	0.81[ASN][1000 genomes]
rs9425773	0.87[ASN][1000 genomes]
rs9425775	0.88[ASN][1000 genomes]
rs9425779	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425780	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs961148	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs965498	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9728376	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
3	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv3407396	chr1:173896346-173917122	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12086019	SERPINC1	cis	Muscle Skeletal	GTEx
rs12086019	SERPINC1	cis	Esophagus Muscularis	GTEx
rs12086019	SERPINC1	cis	Esophagus Mucosa	GTEx
rs12086019	SERPINC1	cis	Thyroid	GTEx
rs12086019	SERPINC1	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:173894600-173914400	Weak transcription	Right Ventricle	heart
3	chr1:173895200-173912200	Weak transcription	Stomach Mucosa	stomach
4	chr1:173896400-173914400	Weak transcription	Pancreas	Pancrea
5	chr1:173898000-173915200	Weak transcription	Aorta	Aorta
6	chr1:173898200-173912200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:173898800-173912200	Weak transcription	NHEK	skin
8	chr1:173899200-173913800	Weak transcription	Fetal Heart	heart
9	chr1:173899400-173917400	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:173899400-173927200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:173899400-173929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:173899600-173923200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:173899800-173953800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:173900000-173929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:173900000-173958600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:173900200-173912400	Weak transcription	Fetal Brain Male	brain
20	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:173901200-173931400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:173901600-173912800	Strong transcription	HSMM	muscle
26	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:173901600-173966400	Strong transcription	Dnd41	blood
28	chr1:173902200-173921200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:173902200-173928200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:173902200-173954600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:173902600-173954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:173903200-173925000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:173903200-173925600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:173903400-173915600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:173903400-173917400	Strong transcription	HUVEC	blood vessel
36	chr1:173903400-173927000	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:173903400-173927000	Strong transcription	Fetal Thymus	thymus
38	chr1:173903800-173912600	Weak transcription	Brain Angular Gyrus	brain
39	chr1:173904000-173929200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:173904200-173912400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:173904800-173921400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:173904800-173921400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:173904800-173923200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:173904800-173954200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:173905000-173927000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:173905000-173938400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:173905200-173954600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:173906000-173920800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links