Variant report

Variant	rs12087212
Chromosome Location	chr1:173898937-173898938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173834350..173837246-chr1:173897897..173899668,2	K562	blood:
2	chr1:173894161..173896195-chr1:173897803..173900471,2	K562	blood:
3	chr1:173893484..173896039-chr1:173897096..173899356,2	MCF-7	breast:
4	chr1:173898854..173900882-chr1:173905926..173908293,2	MCF-7	breast:
5	chr1:173833906..173839819-chr1:173898429..173906150,11	MCF-7	breast:

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

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10494491	0.81[EUR][1000 genomes]
rs10912702	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10912710	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10912716	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10912717	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10912721	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12029025	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12058585	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12060331	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12060401	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12063266	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12067580	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12069129	0.94[AMR][1000 genomes]
rs12071784	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12072602	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12072905	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12077782	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12077812	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12083593	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12085939	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12086019	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12086826	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12089005	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12089405	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12093885	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12562588	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12562959	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12565352	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12565973	0.81[EUR][1000 genomes]
rs12566022	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566642	0.81[EUR][1000 genomes]
rs12566651	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12566842	0.81[EUR][1000 genomes]
rs1321637	0.81[EUR][1000 genomes]
rs13375205	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1407596	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1407597	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16846641	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1987871	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1987873	0.81[ASN][1000 genomes]
rs2009083	0.86[AMR][1000 genomes]
rs2025241	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2227588	0.80[ASN][1000 genomes]
rs2227601	0.90[AMR][1000 genomes]
rs28595073	0.83[EUR][1000 genomes]
rs2860841	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2901784	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36013663	0.83[EUR][1000 genomes]
rs3980286	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4536054	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56926540	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57849055	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59520434	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59960208	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60551050	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826771	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61826774	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826779	0.81[EUR][1000 genomes]
rs61826785	0.83[EUR][1000 genomes]
rs61826823	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61826824	0.81[EUR][1000 genomes]
rs61826829	0.81[EUR][1000 genomes]
rs61826831	0.81[EUR][1000 genomes]
rs61827957	0.84[ASN][1000 genomes]
rs61827959	0.92[ASN][1000 genomes]
rs61828895	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828898	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828899	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828900	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61828901	0.85[ASN][1000 genomes]
rs6425262	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425264	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425266	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6425267	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6425271	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6425272	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6657380	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6661182	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6665720	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6665880	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6668543	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6676307	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6680088	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6683276	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6684527	0.83[EUR][1000 genomes]
rs6688176	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6695887	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6698123	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6702454	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6703547	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs724416	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7523504	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7528380	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7530661	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7547880	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7549291	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs767053	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283385	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9286896	0.92[AMR][1000 genomes]
rs9425773	0.86[ASN][1000 genomes]
rs9425775	0.87[ASN][1000 genomes]
rs9425779	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425780	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs961148	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs965498	0.81[EUR][1000 genomes]
rs9728376	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12087212	SERPINC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
3	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
4	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
5	chr1:173874400-173899800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:173879200-173899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:173888400-173900200	Weak transcription	Right Atrium	heart
9	chr1:173891200-173899400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:173893400-173908400	Weak transcription	Colonic Mucosa	Colon
11	chr1:173894000-173904800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:173894400-173905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:173894600-173899200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:173894600-173907800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:173894600-173914400	Weak transcription	Right Ventricle	heart
16	chr1:173895000-173902400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:173895000-173903400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:173895200-173900000	Weak transcription	A549	lung
19	chr1:173895200-173912200	Weak transcription	Stomach Mucosa	stomach
20	chr1:173895400-173900000	Weak transcription	K562	blood
21	chr1:173895400-173907600	Weak transcription	Ovary	ovary
22	chr1:173895600-173901200	Weak transcription	HUVEC	blood vessel
23	chr1:173895600-173906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:173895800-173906200	Weak transcription	HepG2	liver
25	chr1:173896000-173899400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:173896000-173899600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:173896400-173901400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:173896400-173902800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:173896400-173907800	Weak transcription	Gastric	stomach
30	chr1:173896400-173910000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:173896400-173914400	Weak transcription	Pancreas	Pancrea
32	chr1:173896600-173899400	Weak transcription	Fetal Intestine Large	intestine
33	chr1:173896600-173902800	Weak transcription	Adipose Nuclei	Adipose
34	chr1:173896800-173908400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:173897000-173907800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:173897000-173908400	Weak transcription	Fetal Intestine Small	intestine
37	chr1:173897200-173899600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:173897400-173899400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:173897400-173907200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:173897600-173899800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr1:173897600-173900000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:173897600-173903600	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:173897600-173907200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:173897800-173899400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:173897800-173899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:173897800-173899400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:173897800-173899400	Weak transcription	Esophagus	oesophagus
48	chr1:173897800-173900000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:173897800-173900000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:173897800-173900200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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