Variant report

Variant	rs12120797
Chromosome Location	chr1:180752928-180752929
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	chr1:180745041..180748081-chr1:180751703..180755514,3	MCF-7	breast:
2	chr1:180752587..180754098-chr1:180771744..180774694,2	K562	blood:

Extended variants
information (count: 151 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1043069	0.85[ASN][1000 genomes]
rs10494532	0.84[ASN][1000 genomes]
rs1061015	0.88[ASN][1000 genomes]
rs1061016	0.88[ASN][1000 genomes]
rs10737351	0.94[ASN][1000 genomes]
rs10753223	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10753224	0.87[ASN][1000 genomes]
rs10753225	0.93[ASN][1000 genomes]
rs10798788	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10798789	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798790	0.87[ASN][1000 genomes]
rs10798792	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10798793	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798794	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10798795	0.85[ASN][1000 genomes]
rs10914074	0.84[ASN][1000 genomes]
rs10914076	0.84[ASN][1000 genomes]
rs10914077	0.86[ASN][1000 genomes]
rs10914078	0.86[ASN][1000 genomes]
rs10914079	0.86[ASN][1000 genomes]
rs10914080	0.86[ASN][1000 genomes]
rs10914083	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10914084	0.84[ASN][1000 genomes]
rs10914095	0.93[ASN][1000 genomes]
rs10914107	0.93[ASN][1000 genomes]
rs10914108	0.84[ASN][1000 genomes]
rs10914111	0.95[ASN][1000 genomes]
rs10914112	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10914113	0.95[ASN][1000 genomes]
rs10914115	0.94[ASN][1000 genomes]
rs10914117	0.95[ASN][1000 genomes]
rs10914123	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10914124	0.85[ASN][1000 genomes]
rs11585146	0.95[ASN][1000 genomes]
rs11585295	0.87[ASN][1000 genomes]
rs11585424	0.84[ASN][1000 genomes]
rs12022782	0.85[EUR][1000 genomes]
rs12064405	0.82[ASN][1000 genomes]
rs12064862	0.95[ASN][1000 genomes]
rs12064913	0.95[ASN][1000 genomes]
rs12119247	0.93[ASN][1000 genomes]
rs12120511	0.93[ASN][1000 genomes]
rs12120522	0.93[ASN][1000 genomes]
rs12121436	0.92[ASN][1000 genomes]
rs12131056	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12132252	0.83[ASN][1000 genomes]
rs12135869	0.80[ASN][1000 genomes]
rs12137133	0.84[ASN][1000 genomes]
rs12137673	0.93[ASN][1000 genomes]
rs12142163	0.93[ASN][1000 genomes]
rs12143462	0.83[ASN][1000 genomes]
rs12143674	0.85[ASN][1000 genomes]
rs12143915	0.93[ASN][1000 genomes]
rs12562489	0.86[EUR][1000 genomes]
rs12564487	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12725006	0.95[ASN][1000 genomes]
rs12733315	0.84[ASN][1000 genomes]
rs1339769	0.90[ASN][1000 genomes]
rs1533422	0.95[ASN][1000 genomes]
rs1554183	0.94[ASN][1000 genomes]
rs1554184	0.93[ASN][1000 genomes]
rs1554185	0.93[ASN][1000 genomes]
rs17373584	0.83[ASN][1000 genomes]
rs1973674	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980157	0.92[ASN][1000 genomes]
rs2027354	0.80[ASN][1000 genomes]
rs2138399	0.95[ASN][1000 genomes]
rs2176183	0.93[ASN][1000 genomes]
rs2176184	0.95[ASN][1000 genomes]
rs2271669	0.95[ASN][1000 genomes]
rs2331887	0.93[ASN][1000 genomes]
rs2944261	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3002118	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002119	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34111145	0.93[ASN][1000 genomes]
rs3761903	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3761904	0.84[ASN][1000 genomes]
rs3789367	0.93[ASN][1000 genomes]
rs3789368	0.93[ASN][1000 genomes]
rs3789369	0.93[ASN][1000 genomes]
rs3789370	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789373	0.93[ASN][1000 genomes]
rs3845407	0.84[ASN][1000 genomes]
rs3856059	0.83[ASN][1000 genomes]
rs3856060	0.93[ASN][1000 genomes]
rs3903979	0.84[ASN][1000 genomes]
rs3908048	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4259606	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4265395	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4326588	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4454505	0.92[ASN][1000 genomes]
rs4550006	0.87[ASN][1000 genomes]
rs4598454	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4652525	0.84[ASN][1000 genomes]
rs4652526	0.85[ASN][1000 genomes]
rs4652527	0.92[ASN][1000 genomes]
rs4652528	0.92[ASN][1000 genomes]
rs4652529	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652530	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652531	0.95[ASN][1000 genomes]
rs4652533	0.93[ASN][1000 genomes]
rs4652535	0.93[ASN][1000 genomes]
rs61809343	0.84[ASN][1000 genomes]
rs61811244	0.85[ASN][1000 genomes]
rs6425655	0.93[ASN][1000 genomes]
rs6661417	0.93[ASN][1000 genomes]
rs6677349	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6677570	0.84[ASN][1000 genomes]
rs6677681	0.84[ASN][1000 genomes]
rs6688486	0.84[ASN][1000 genomes]
rs6689104	0.95[ASN][1000 genomes]
rs6699726	0.86[ASN][1000 genomes]
rs6700926	0.96[EUR][1000 genomes]
rs6702006	0.83[EUR][1000 genomes]
rs6703189	0.93[ASN][1000 genomes]
rs7349119	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7516646	0.93[ASN][1000 genomes]
rs7536258	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7544774	0.84[ASN][1000 genomes]
rs7546227	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7546516	0.93[ASN][1000 genomes]
rs7548261	0.89[ASN][1000 genomes]
rs7548671	0.92[ASN][1000 genomes]
rs7555356	0.93[ASN][1000 genomes]
rs7556592	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9661675	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9701903	0.91[ASN][1000 genomes]
rs9919167	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv3777	chr1:180741213-180780313	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv548346	chr1:180747033-180755321	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3492942	chr1:180748679-180756477	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3492947	chr1:180749054-180756402	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3492945	chr1:180749543-180756750	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3492946	chr1:180749637-180755448	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3452584	chr1:180749640-180755552	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3492943	chr1:180749676-180755458	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3492944	chr1:180749764-180755403	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv498695	chr1:180749768-180755398	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3452585	chr1:180749769-180755398	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3492948	chr1:180749769-180755398	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv20795	chr1:180750406-180755506	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv548347	chr1:180750481-180754933	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv548348	chr1:180750481-180755259	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv548349	chr1:180750481-180755321	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv548350	chr1:180750701-180755188	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv548351	chr1:180750701-180755321	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv548352	chr1:180751409-180755259	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv548353	chr1:180751409-180755321	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv548354	chr1:180751636-180755321	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv548355	chr1:180752625-180755321	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180713000-180814200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:180740200-180753000	Weak transcription	Small Intestine	intestine
3	chr1:180740200-180761000	Weak transcription	Psoas Muscle	Psoas
4	chr1:180740800-180775600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:180741000-180757200	Weak transcription	Primary B cells from cord blood	blood
6	chr1:180741600-180784000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:180743400-180757200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:180743400-180763000	Weak transcription	HSMM	muscle
9	chr1:180744000-180757200	Weak transcription	Primary T cells from cord blood	blood
10	chr1:180747000-180756800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:180747800-180761000	Weak transcription	Aorta	Aorta
12	chr1:180748200-180755800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:180749400-180761200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:180749600-180761200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:180751000-180753000	Enhancers	Left Ventricle	heart
16	chr1:180751400-180774600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:180751800-180754000	Weak transcription	Fetal Brain Male	brain
18	chr1:180751800-180755000	Weak transcription	Fetal Brain Female	brain
19	chr1:180752800-180753200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links