Variant report

Variant	rs12463548
Chromosome Location	chr2:30704981-30704982
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	chr2:30704716..30706255-chr2:30708517..30710606,2	MCF-7	breast:
2	chr2:30703972..30706142-chr2:30708659..30711183,2	MCF-7	breast:

Extended variants
information (count: 160 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10169001	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169512	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170012	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10174170	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10176138	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178307	0.83[EUR][1000 genomes]
rs10178829	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180054	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181161	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10186917	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10197915	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10198587	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200589	0.82[EUR][1000 genomes]
rs10200895	0.83[EUR][1000 genomes]
rs10201020	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10204301	0.88[EUR][1000 genomes]
rs10206659	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10206668	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208299	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208587	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210365	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10211659	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10469986	0.83[EUR][1000 genomes]
rs10469987	0.83[EUR][1000 genomes]
rs10514772	0.83[EUR][1000 genomes]
rs1074066	0.83[EUR][1000 genomes]
rs11127277	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11127279	0.88[EUR][1000 genomes]
rs11885407	0.86[EUR][1000 genomes]
rs11886181	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11896768	0.83[EUR][1000 genomes]
rs11899182	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11901989	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903573	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12465894	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12466071	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12466818	0.82[EUR][1000 genomes]
rs12467017	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467646	0.83[EUR][1000 genomes]
rs12467830	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467831	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12468971	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12469630	0.83[EUR][1000 genomes]
rs12469745	0.83[EUR][1000 genomes]
rs12469849	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471248	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471868	0.82[EUR][1000 genomes]
rs12474202	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12475104	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12476387	0.88[EUR][1000 genomes]
rs12476392	0.88[EUR][1000 genomes]
rs12476805	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12477267	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12478778	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13382540	0.90[ASN][1000 genomes]
rs13383939	0.83[EUR][1000 genomes]
rs13388031	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13388156	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13388701	0.82[EUR][1000 genomes]
rs13389142	0.83[EUR][1000 genomes]
rs13390344	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13391492	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13393150	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397800	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13398796	0.83[EUR][1000 genomes]
rs13401246	0.87[EUR][1000 genomes]
rs13404307	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405340	0.82[EUR][1000 genomes]
rs13408621	0.82[EUR][1000 genomes]
rs13412012	0.88[EUR][1000 genomes]
rs13413678	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413980	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13414468	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13417949	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13419209	0.82[EUR][1000 genomes]
rs13419435	0.82[EUR][1000 genomes]
rs13422024	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13424441	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13427862	0.83[EUR][1000 genomes]
rs13428342	0.83[EUR][1000 genomes]
rs13430515	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430622	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430781	0.83[EUR][1000 genomes]
rs13432085	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1404607	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17009601	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17009805	0.86[EUR][1000 genomes]
rs17009808	0.88[EUR][1000 genomes]
rs1869425	0.83[EUR][1000 genomes]
rs1869426	0.83[EUR][1000 genomes]
rs1880539	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1880541	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1982286	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1997036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997037	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028668	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2077985	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2084301	0.83[EUR][1000 genomes]
rs2100112	0.82[EUR][1000 genomes]
rs2100113	0.83[EUR][1000 genomes]
rs2123757	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2166669	0.82[EUR][1000 genomes]
rs2167970	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2363291	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363294	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363311	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2363851	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28378040	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816593	0.82[EUR][1000 genomes]
rs4144806	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4951991	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951993	0.83[EUR][1000 genomes]
rs4951994	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951995	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951996	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951997	0.83[EUR][1000 genomes]
rs4951998	0.83[EUR][1000 genomes]
rs4952000	0.82[EUR][1000 genomes]
rs4952003	0.83[EUR][1000 genomes]
rs4952004	0.83[EUR][1000 genomes]
rs4952126	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952127	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952128	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952129	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952130	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952131	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952132	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952133	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4952135	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952136	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952137	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952139	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952141	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952142	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952143	0.81[ASN][1000 genomes]
rs4952145	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952146	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952149	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952150	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4952152	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952154	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952155	0.86[EUR][1000 genomes]
rs4952158	0.83[EUR][1000 genomes]
rs4952159	0.82[EUR][1000 genomes]
rs4952161	0.83[EUR][1000 genomes]
rs4952162	0.83[EUR][1000 genomes]
rs4952163	0.83[EUR][1000 genomes]
rs4952164	0.83[EUR][1000 genomes]
rs55789733	0.86[EUR][1000 genomes]
rs6723023	0.82[EUR][1000 genomes]
rs6739248	0.83[EUR][1000 genomes]
rs7355326	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7355456	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597579	0.83[EUR][1000 genomes]
rs7603834	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603947	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605131	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs766880	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9309681	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12463548	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30678600-30710600	Weak transcription	NHLF	lung
2	chr2:30688600-30710000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:30695200-30707000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:30695600-30705400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:30695800-30706600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:30696200-30710600	Weak transcription	Ovary	ovary
7	chr2:30697400-30710400	Weak transcription	Fetal Kidney	kidney
8	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
9	chr2:30698000-30708000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:30698000-30709400	Weak transcription	Pancreas	Pancrea
11	chr2:30698200-30710600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:30698400-30706800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr2:30699000-30709600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:30699000-30711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:30699600-30709400	Weak transcription	Right Ventricle	heart
16	chr2:30701200-30705600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:30701200-30714400	Weak transcription	HSMM	muscle
18	chr2:30702800-30710400	Weak transcription	Primary T cells from cord blood	blood
19	chr2:30703600-30705000	Enhancers	GM12878-XiMat	blood
20	chr2:30703600-30706000	Enhancers	Fetal Heart	heart
21	chr2:30703600-30706000	Enhancers	Small Intestine	intestine
22	chr2:30704200-30705000	Enhancers	Fetal Lung	lung
23	chr2:30704200-30705000	Enhancers	Osteobl	bone
24	chr2:30704200-30705600	Enhancers	Fetal Stomach	stomach
25	chr2:30704200-30705800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:30704200-30705800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:30704200-30706000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:30704200-30706000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr2:30704400-30705000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:30704400-30705000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:30704400-30705000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:30704400-30705400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:30704400-30705600	Enhancers	Stomach Smooth Muscle	stomach
34	chr2:30704400-30706200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr2:30704600-30705000	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr2:30704600-30705200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr2:30704600-30705400	Weak transcription	Fetal Intestine Large	intestine
38	chr2:30704600-30705600	Weak transcription	Fetal Intestine Small	intestine
39	chr2:30704600-30706600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:30704600-30707000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:30704600-30709400	Weak transcription	Left Ventricle	heart
42	chr2:30704600-30710600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:30704600-30710600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:30704600-30715800	Weak transcription	Psoas Muscle	Psoas
45	chr2:30704600-30719600	Weak transcription	Right Atrium	heart
46	chr2:30704600-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:30704600-30720600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:30704800-30705200	Weak transcription	Aorta	Aorta
49	chr2:30704800-30705200	Enhancers	Duodenum Mucosa	Duodenum
50	chr2:30704800-30705800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links