Variant report

Variant	rs10180054
Chromosome Location	chr2:30705622-30705623
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	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: 161 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10169001	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169512	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170012	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10174170	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10176138	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178307	0.82[EUR][1000 genomes]
rs10178829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181161	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10186917	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10197915	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10198587	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200589	0.81[EUR][1000 genomes]
rs10200895	0.82[EUR][1000 genomes]
rs10201020	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10204301	0.87[EUR][1000 genomes]
rs10206659	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10206668	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208299	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208587	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210365	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10211659	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10469986	0.82[EUR][1000 genomes]
rs10469987	0.82[EUR][1000 genomes]
rs10514772	0.82[EUR][1000 genomes]
rs1074066	0.82[EUR][1000 genomes]
rs11127277	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11127279	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11885407	0.85[EUR][1000 genomes]
rs11886181	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11896768	0.82[EUR][1000 genomes]
rs11899182	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11901989	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903573	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12463548	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465894	0.83[EUR][1000 genomes]
rs12466071	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12466818	0.81[EUR][1000 genomes]
rs12467017	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467646	0.82[EUR][1000 genomes]
rs12467830	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467831	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12468971	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12469630	0.82[EUR][1000 genomes]
rs12469745	0.82[EUR][1000 genomes]
rs12469849	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471868	0.81[EUR][1000 genomes]
rs12474202	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12475104	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12476387	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12476392	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12476805	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12477267	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12478778	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13382540	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13383939	0.82[EUR][1000 genomes]
rs13388031	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13388156	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13388701	0.81[EUR][1000 genomes]
rs13389142	0.82[EUR][1000 genomes]
rs13390344	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13391492	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13393150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397800	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13398796	0.82[EUR][1000 genomes]
rs13401246	0.86[EUR][1000 genomes]
rs13404307	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405340	0.81[EUR][1000 genomes]
rs13408621	0.81[EUR][1000 genomes]
rs13412012	0.87[EUR][1000 genomes]
rs13413678	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413980	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13414468	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13417949	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13419209	0.81[EUR][1000 genomes]
rs13419435	0.81[EUR][1000 genomes]
rs13422024	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13424441	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13427862	0.82[EUR][1000 genomes]
rs13428342	0.82[EUR][1000 genomes]
rs13430515	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430622	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430781	0.82[EUR][1000 genomes]
rs13432085	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1404607	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17009601	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17009805	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17009808	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1869425	0.82[EUR][1000 genomes]
rs1869426	0.82[EUR][1000 genomes]
rs1880539	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1880541	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1982286	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1997036	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997037	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028668	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2077985	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2084301	0.82[EUR][1000 genomes]
rs2100112	0.81[EUR][1000 genomes]
rs2100113	0.82[EUR][1000 genomes]
rs2123757	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2166669	0.81[EUR][1000 genomes]
rs2167970	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2363291	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363294	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363311	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2363851	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28378040	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816593	0.81[EUR][1000 genomes]
rs4144806	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4951991	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951993	0.84[EUR][1000 genomes]
rs4951994	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951995	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951996	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951997	0.82[EUR][1000 genomes]
rs4951998	0.82[EUR][1000 genomes]
rs4952000	0.81[EUR][1000 genomes]
rs4952003	0.82[EUR][1000 genomes]
rs4952004	0.82[EUR][1000 genomes]
rs4952126	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952127	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952128	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952132	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952133	0.85[AMR][1000 genomes]
rs4952135	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952136	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952137	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952139	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952141	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952142	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952143	0.81[ASN][1000 genomes]
rs4952145	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952146	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952149	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952150	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4952151	0.82[AFR][1000 genomes]
rs4952152	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952154	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952155	0.85[EUR][1000 genomes]
rs4952158	0.82[EUR][1000 genomes]
rs4952159	0.81[EUR][1000 genomes]
rs4952161	0.82[EUR][1000 genomes]
rs4952162	0.82[EUR][1000 genomes]
rs4952163	0.82[EUR][1000 genomes]
rs4952164	0.82[EUR][1000 genomes]
rs55789733	0.85[EUR][1000 genomes]
rs6723023	0.81[EUR][1000 genomes]
rs6739248	0.82[EUR][1000 genomes]
rs7355326	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7355456	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597579	0.82[EUR][1000 genomes]
rs7603834	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603947	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605131	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs766880	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9309681	0.85[AFR][1000 genomes];0.86[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
rs10180054	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 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	chr2:30695800-30706600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:30696200-30710600	Weak transcription	Ovary	ovary
6	chr2:30697400-30710400	Weak transcription	Fetal Kidney	kidney
7	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
8	chr2:30698000-30708000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:30698000-30709400	Weak transcription	Pancreas	Pancrea
10	chr2:30698200-30710600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:30698400-30706800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:30699000-30709600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:30699000-30711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:30699600-30709400	Weak transcription	Right Ventricle	heart
15	chr2:30701200-30714400	Weak transcription	HSMM	muscle
16	chr2:30702800-30710400	Weak transcription	Primary T cells from cord blood	blood
17	chr2:30703600-30706000	Enhancers	Fetal Heart	heart
18	chr2:30703600-30706000	Enhancers	Small Intestine	intestine
19	chr2:30704200-30705800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:30704200-30705800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:30704200-30706000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:30704200-30706000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr2:30704400-30706200	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:30704600-30706600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:30704600-30707000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:30704600-30709400	Weak transcription	Left Ventricle	heart
27	chr2:30704600-30710600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:30704600-30710600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:30704600-30715800	Weak transcription	Psoas Muscle	Psoas
30	chr2:30704600-30719600	Weak transcription	Right Atrium	heart
31	chr2:30704600-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:30704600-30720600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:30704800-30705800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:30704800-30707000	Weak transcription	Primary B cells from cord blood	blood
35	chr2:30704800-30707000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:30704800-30707000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:30704800-30708600	Weak transcription	K562	blood
38	chr2:30704800-30710400	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:30704800-30710800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:30704800-30714200	Weak transcription	HSMMtube	muscle
41	chr2:30704800-30714400	Weak transcription	A549	lung
42	chr2:30705000-30706600	Weak transcription	GM12878-XiMat	blood
43	chr2:30705000-30709400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:30705200-30705800	Enhancers	Aorta	Aorta
45	chr2:30705200-30710400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr2:30705400-30710400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:30705600-30705800	Enhancers	Fetal Intestine Small	intestine
48	chr2:30705600-30708000	Weak transcription	Fetal Stomach	stomach
49	chr2:30705600-30710200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:30705600-30710600	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links