Variant report

Variant	rs12069129
Chromosome Location	chr1:173935779-173935780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173931023..173932801-chr1:173933873..173936006,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10494491	0.84[ASN][1000 genomes]
rs10912702	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10912710	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10912716	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10912717	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10912721	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12029025	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12058585	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12060331	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12060401	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12063266	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12067580	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12071784	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12072602	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12072905	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12077782	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12077812	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12083593	0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12085939	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12086019	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12086826	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12087212	0.94[AMR][1000 genomes]
rs12089005	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12089405	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12093885	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12562588	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12562959	0.94[ASN][1000 genomes]
rs12565352	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12565973	0.86[ASN][1000 genomes]
rs12566022	0.93[ASN][1000 genomes]
rs12566642	0.89[ASN][1000 genomes]
rs12566651	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12566842	0.89[ASN][1000 genomes]
rs1321637	0.86[ASN][1000 genomes]
rs13375205	0.93[ASN][1000 genomes]
rs1407596	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1407597	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16846641	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1987871	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1987873	0.88[ASN][1000 genomes]
rs2009083	0.92[AMR][1000 genomes]
rs2025241	0.93[ASN][1000 genomes]
rs2227590	0.84[AMR][1000 genomes]
rs2227593	0.84[AMR][1000 genomes]
rs2227594	0.82[AMR][1000 genomes]
rs2227597	0.84[AMR][1000 genomes]
rs2227601	0.96[AMR][1000 genomes]
rs2295958	0.81[AMR][1000 genomes]
rs28595073	0.81[ASN][1000 genomes]
rs2860841	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2901784	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs36013663	0.82[ASN][1000 genomes]
rs3980286	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4536054	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56926540	0.91[ASN][1000 genomes]
rs57849055	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58092103	0.84[ASN][1000 genomes]
rs59520434	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59960208	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60551050	0.91[ASN][1000 genomes]
rs61826771	0.94[ASN][1000 genomes]
rs61826774	0.91[ASN][1000 genomes]
rs61826777	0.89[ASN][1000 genomes]
rs61826779	0.89[ASN][1000 genomes]
rs61826780	0.85[ASN][1000 genomes]
rs61826784	0.89[ASN][1000 genomes]
rs61826785	0.86[ASN][1000 genomes]
rs61826823	0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61826824	0.84[ASN][1000 genomes]
rs61826826	0.85[ASN][1000 genomes]
rs61826829	0.81[ASN][1000 genomes]
rs61826831	0.81[ASN][1000 genomes]
rs61827959	0.87[ASN][1000 genomes]
rs61828895	0.93[ASN][1000 genomes]
rs61828898	0.93[ASN][1000 genomes]
rs61828899	0.93[ASN][1000 genomes]
rs61828900	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61828901	0.94[ASN][1000 genomes]
rs6425262	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6425264	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6425266	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6425267	0.98[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6425271	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6425272	0.89[AMR][1000 genomes]
rs6657380	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6661182	0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6665720	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6665880	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6668543	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6676307	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6680088	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6683276	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6684527	0.81[ASN][1000 genomes]
rs6688176	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6695887	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6698123	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6702454	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6703547	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs724416	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7523504	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7528380	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7530661	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7547880	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7549291	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs767053	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9283385	0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9286896	0.98[AMR][1000 genomes]
rs9425773	0.82[ASN][1000 genomes]
rs9425775	0.82[ASN][1000 genomes]
rs9425779	0.87[ASN][1000 genomes]
rs9425780	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs961148	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs965498	0.81[ASN][1000 genomes]
rs9728376	0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	nsv872550	chr1:173913804-173964206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12069129	SERPINC1	cis	Esophagus Mucosa	GTEx
rs12069129	SERPINC1	cis	Esophagus Muscularis	GTEx
rs12069129	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173899800-173953800	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr1:173900000-173958600	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:173901600-173966400	Strong transcription	Dnd41	blood
12	chr1:173902200-173954600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr1:173902600-173954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:173904800-173954200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:173905000-173938400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:173905200-173954600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:173906000-173940400	Strong transcription	Adipose Nuclei	Adipose
20	chr1:173906000-173959000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:173906200-173937600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:173906800-173959000	Strong transcription	Liver	Liver
23	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:173910400-173952200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
26	chr1:173922200-173942000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:173922200-173954000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:173922600-173936400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:173923400-173954400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:173923400-173962400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:173923600-173939800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:173923800-173953800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:173923800-173954400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:173923800-173955600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:173924000-173940200	Strong transcription	Osteobl	bone
36	chr1:173925200-173937600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:173926600-173938400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:173927600-173954200	Strong transcription	Placenta	Placenta
39	chr1:173928200-173936600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:173928200-173938400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:173928400-173936800	Strong transcription	Primary T cells from cord blood	blood
42	chr1:173928600-173936400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:173928600-173936600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:173928600-173936600	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:173928600-173938400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:173928600-173940200	Strong transcription	Fetal Thymus	thymus
47	chr1:173928600-173942200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:173928800-173953800	Strong transcription	Fetal Intestine Large	intestine
49	chr1:173929000-173937000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:173929000-173937400	Strong transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links