Variant report

Variant	rs4952139
Chromosome Location	chr2:30742711-30742712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30742633..30745818-chr2:30753474..30756226,3	K562	blood:
2	chr2:30740997..30743225-chr2:30749540..30752188,2	MCF-7	breast:

Extended variants
information (count: 158 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10169001	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10169512	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10170012	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174170	0.85[ASN][1000 genomes]
rs10176138	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10178307	0.86[EUR][1000 genomes]
rs10178829	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10180054	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10181161	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10186917	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10197915	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10198587	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10200589	0.85[EUR][1000 genomes]
rs10200895	0.86[EUR][1000 genomes]
rs10201020	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10204301	0.92[EUR][1000 genomes]
rs10206659	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10206668	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10208299	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10208587	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10210365	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10211659	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10469986	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10469987	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514772	0.86[EUR][1000 genomes]
rs1074066	0.86[EUR][1000 genomes]
rs11127277	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11127279	0.92[EUR][1000 genomes]
rs11885407	0.90[EUR][1000 genomes]
rs11886181	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11896768	0.86[EUR][1000 genomes]
rs11899182	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11901989	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11903573	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12463548	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12465894	0.87[EUR][1000 genomes]
rs12466071	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12466818	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467017	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467646	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467830	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467831	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12468971	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469630	0.86[EUR][1000 genomes]
rs12469745	0.86[EUR][1000 genomes]
rs12469849	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12471248	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12471868	0.85[EUR][1000 genomes]
rs12474202	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12475104	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12476387	0.92[EUR][1000 genomes]
rs12476392	0.92[EUR][1000 genomes]
rs12476805	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12477267	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12478778	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13383939	0.86[EUR][1000 genomes]
rs13388031	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13388156	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13388701	0.85[EUR][1000 genomes]
rs13389142	0.86[EUR][1000 genomes]
rs13390344	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13391492	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13393150	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13397800	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13398796	0.86[EUR][1000 genomes]
rs13401246	0.91[EUR][1000 genomes]
rs13404307	0.84[ASN][1000 genomes]
rs13405340	0.85[EUR][1000 genomes]
rs13408621	0.85[EUR][1000 genomes]
rs13412012	0.92[EUR][1000 genomes]
rs13413678	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13413980	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13414468	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13417949	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13419209	0.87[EUR][1000 genomes]
rs13419435	0.87[EUR][1000 genomes]
rs13422024	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13424441	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13427862	0.86[EUR][1000 genomes]
rs13428342	0.86[EUR][1000 genomes]
rs13430515	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13430622	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13430781	0.86[EUR][1000 genomes]
rs13432085	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404607	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17009601	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009805	0.90[EUR][1000 genomes]
rs17009808	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1869425	0.86[EUR][1000 genomes]
rs1869426	0.86[EUR][1000 genomes]
rs1880539	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1880541	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1982286	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1997036	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1997037	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2028668	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2077985	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2084301	0.86[EUR][1000 genomes]
rs2100112	0.85[EUR][1000 genomes]
rs2100113	0.86[EUR][1000 genomes]
rs2123757	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2166669	0.85[EUR][1000 genomes]
rs2167970	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2363291	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2363294	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2363311	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2363851	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28378040	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3816593	0.85[EUR][1000 genomes]
rs4144806	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4951991	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951993	0.91[EUR][1000 genomes]
rs4951994	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951995	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951996	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951997	0.86[EUR][1000 genomes]
rs4951998	0.86[EUR][1000 genomes]
rs4952000	0.85[EUR][1000 genomes]
rs4952003	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952004	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4952126	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952127	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952128	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952129	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952130	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952131	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952132	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952135	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4952136	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952137	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952141	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952142	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4952143	0.81[EUR][1000 genomes]
rs4952145	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952146	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952149	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952150	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4952152	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952154	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952155	0.90[EUR][1000 genomes]
rs4952158	0.86[EUR][1000 genomes]
rs4952159	0.85[EUR][1000 genomes]
rs4952161	0.86[EUR][1000 genomes]
rs4952162	0.86[EUR][1000 genomes]
rs4952163	0.86[EUR][1000 genomes]
rs4952164	0.86[EUR][1000 genomes]
rs55789733	0.90[EUR][1000 genomes]
rs6723023	0.85[EUR][1000 genomes]
rs6739248	0.86[EUR][1000 genomes]
rs7355326	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7355456	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597579	0.86[EUR][1000 genomes]
rs7603834	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7603947	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7605131	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs766880	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9309681	0.91[EUR][1000 genomes];0.83[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
rs4952139	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30729000-30764600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:30733000-30756000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:30734800-30764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:30735600-30742800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:30736800-30752400	Weak transcription	Psoas Muscle	Psoas
6	chr2:30738000-30750400	Weak transcription	Liver	Liver
7	chr2:30738000-30757000	Weak transcription	Ovary	ovary
8	chr2:30738200-30742800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:30738200-30744000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:30738200-30750000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:30738200-30750800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:30738200-30750800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:30738200-30751000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:30738200-30752400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:30738200-30758200	Weak transcription	Right Ventricle	heart
16	chr2:30738400-30748600	Weak transcription	Fetal Kidney	kidney
17	chr2:30738400-30756200	Weak transcription	Hela-S3	cervix
18	chr2:30741000-30745200	Weak transcription	Fetal Heart	heart
19	chr2:30741200-30743000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr2:30741400-30743000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:30741400-30743000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:30741400-30743400	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr2:30741400-30743400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:30741400-30743600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:30741400-30744200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:30741600-30742800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
27	chr2:30741600-30743000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:30741600-30743200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr2:30741600-30743200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
30	chr2:30741600-30743200	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr2:30741600-30743200	ZNF genes & repeats	Fetal Thymus	thymus
32	chr2:30741600-30743600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
33	chr2:30741600-30744000	ZNF genes & repeats	Thymus	Thymus
34	chr2:30741800-30742800	ZNF genes & repeats	Primary B cells from cord blood	blood
35	chr2:30741800-30743000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:30741800-30743000	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr2:30741800-30743200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:30741800-30743200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr2:30741800-30743200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr2:30741800-30743200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
41	chr2:30741800-30743200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:30741800-30743200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:30741800-30743200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
44	chr2:30741800-30743200	ZNF genes & repeats	Lung	lung
45	chr2:30741800-30743200	ZNF genes & repeats	Dnd41	blood
46	chr2:30741800-30743600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr2:30741800-30744000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr2:30742000-30743000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:30742000-30743000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:30742000-30743000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links