Variant report

Variant	rs61142614
Chromosome Location	chr3:50641420-50641421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50624498..50626370-chr3:50639043..50642026,2	K562	blood:
2	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
3	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114735	Chromatin interaction
ENSG00000088543	Chromatin interaction

Extended variants
information (count: 194 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:185)

rs_ID	r²[population]
rs11130252	0.87[AFR][1000 genomes]
rs11130255	0.87[AFR][1000 genomes]
rs13065995	0.87[AFR][1000 genomes]
rs13072085	0.82[AFR][1000 genomes]
rs13075344	0.87[AFR][1000 genomes]
rs13075377	0.87[AFR][1000 genomes]
rs13084476	0.87[AFR][1000 genomes]
rs13084771	0.87[AFR][1000 genomes]
rs13085096	0.87[AFR][1000 genomes]
rs13088434	0.87[AFR][1000 genomes]
rs13089719	0.87[AFR][1000 genomes]
rs13091933	0.87[AFR][1000 genomes]
rs13093798	0.87[AFR][1000 genomes]
rs13094336	0.87[AFR][1000 genomes]
rs13095920	0.87[AFR][1000 genomes]
rs13096264	0.82[AFR][1000 genomes]
rs13096268	0.87[AFR][1000 genomes]
rs13096772	0.87[AFR][1000 genomes]
rs13099712	0.87[AFR][1000 genomes]
rs13100403	0.87[AFR][1000 genomes]
rs1379873	0.82[AFR][1000 genomes]
rs1379874	0.82[AFR][1000 genomes]
rs1379875	0.82[AFR][1000 genomes]
rs1458386	0.87[AFR][1000 genomes]
rs1458387	0.87[AFR][1000 genomes]
rs1463497	0.87[AFR][1000 genomes]
rs1531271	0.82[AFR][1000 genomes]
rs1563683	0.87[AFR][1000 genomes]
rs1598928	0.82[AFR][1000 genomes]
rs17660179	0.87[AFR][1000 genomes]
rs17660513	0.87[AFR][1000 genomes]
rs17787569	0.87[AFR][1000 genomes]
rs1824280	0.87[AFR][1000 genomes]
rs1841067	0.82[AFR][1000 genomes]
rs1902960	0.87[AFR][1000 genomes]
rs1947607	0.87[AFR][1000 genomes]
rs1966920	0.87[AFR][1000 genomes]
rs2045510	0.87[AFR][1000 genomes]
rs2045511	0.87[AFR][1000 genomes]
rs2061388	0.87[AFR][1000 genomes]
rs2085582	0.82[AFR][1000 genomes]
rs2085584	0.82[AFR][1000 genomes]
rs2085585	0.82[AFR][1000 genomes]
rs2085586	0.82[AFR][1000 genomes]
rs2085587	0.87[AFR][1000 genomes]
rs2125364	0.87[AFR][1000 genomes]
rs2125366	0.87[AFR][1000 genomes]
rs2125369	0.87[AFR][1000 genomes]
rs2168863	0.87[AFR][1000 genomes]
rs2168865	0.82[AFR][1000 genomes]
rs2168866	0.87[AFR][1000 genomes]
rs2199050	0.87[AFR][1000 genomes]
rs2219431	0.82[AFR][1000 genomes]
rs2219432	0.82[AFR][1000 genomes]
rs2227280	0.87[AFR][1000 genomes]
rs2232253	0.87[AFR][1000 genomes]
rs2262810	0.87[AFR][1000 genomes]
rs2269507	0.87[AFR][1000 genomes]
rs2355321	0.87[AFR][1000 genomes]
rs2355341	0.87[AFR][1000 genomes]
rs2355696	0.87[AFR][1000 genomes]
rs2608989	0.87[AFR][1000 genomes]
rs2608993	0.87[AFR][1000 genomes]
rs2608997	0.87[AFR][1000 genomes]
rs2608999	0.87[AFR][1000 genomes]
rs2609001	0.87[AFR][1000 genomes]
rs2609005	0.87[AFR][1000 genomes]
rs2609006	0.87[AFR][1000 genomes]
rs2609016	0.82[AFR][1000 genomes]
rs2609018	0.82[AFR][1000 genomes]
rs2609019	0.82[AFR][1000 genomes]
rs2609020	0.87[AFR][1000 genomes]
rs2609021	0.87[AFR][1000 genomes]
rs2609022	0.87[AFR][1000 genomes]
rs2609024	0.87[AFR][1000 genomes]
rs2609025	0.87[AFR][1000 genomes]
rs2609028	0.82[AFR][1000 genomes]
rs2609035	0.87[AFR][1000 genomes]
rs2609036	0.87[AFR][1000 genomes]
rs2609037	0.87[AFR][1000 genomes]
rs2675769	0.87[AFR][1000 genomes]
rs2675772	0.87[AFR][1000 genomes]
rs2675773	0.87[AFR][1000 genomes]
rs2675774	0.87[AFR][1000 genomes]
rs2675784	0.82[AFR][1000 genomes]
rs2675787	0.87[AFR][1000 genomes]
rs2675788	0.87[AFR][1000 genomes]
rs2675789	0.87[AFR][1000 genomes]
rs2675790	0.87[AFR][1000 genomes]
rs2675791	0.87[AFR][1000 genomes]
rs2675792	0.87[AFR][1000 genomes]
rs2675793	0.87[AFR][1000 genomes]
rs2675794	0.87[AFR][1000 genomes]
rs2675799	0.82[AFR][1000 genomes]
rs2675800	0.87[AFR][1000 genomes]
rs2675802	0.87[AFR][1000 genomes]
rs2675804	0.87[AFR][1000 genomes]
rs2675806	0.87[AFR][1000 genomes]
rs2675809	0.87[AFR][1000 genomes]
rs2675810	0.87[AFR][1000 genomes]
rs2675812	0.87[AFR][1000 genomes]
rs2675813	0.87[AFR][1000 genomes]
rs2675819	0.82[AFR][1000 genomes]
rs2675821	0.82[AFR][1000 genomes]
rs2675822	0.82[AFR][1000 genomes]
rs2675825	0.82[AFR][1000 genomes]
rs2675827	0.87[AFR][1000 genomes]
rs2675828	0.87[AFR][1000 genomes]
rs2675829	0.87[AFR][1000 genomes]
rs2675830	0.87[AFR][1000 genomes]
rs2675832	0.87[AFR][1000 genomes]
rs2675834	0.87[AFR][1000 genomes]
rs2675835	0.82[AFR][1000 genomes]
rs2675836	0.87[AFR][1000 genomes]
rs2675837	0.87[AFR][1000 genomes]
rs3101107	0.87[AFR][1000 genomes]
rs3106826	0.87[AFR][1000 genomes]
rs34048522	0.87[AFR][1000 genomes]
rs34202063	0.87[AFR][1000 genomes]
rs34266990	0.87[AFR][1000 genomes]
rs34320663	0.87[AFR][1000 genomes]
rs34390947	0.87[AFR][1000 genomes]
rs34399912	0.87[AFR][1000 genomes]
rs34576538	0.87[AFR][1000 genomes]
rs34584636	0.87[AFR][1000 genomes]
rs34632971	0.87[AFR][1000 genomes]
rs34756253	0.87[AFR][1000 genomes]
rs34773360	0.87[AFR][1000 genomes]
rs34846525	0.87[AFR][1000 genomes]
rs34866096	0.87[AFR][1000 genomes]
rs34889917	0.87[AFR][1000 genomes]
rs35098074	0.87[AFR][1000 genomes]
rs35140911	0.87[AFR][1000 genomes]
rs35170043	0.87[AFR][1000 genomes]
rs35429015	0.87[AFR][1000 genomes]
rs35531616	0.87[AFR][1000 genomes]
rs35566897	0.87[AFR][1000 genomes]
rs35655236	0.87[AFR][1000 genomes]
rs35690191	0.87[AFR][1000 genomes]
rs36057916	0.82[AFR][1000 genomes]
rs3804628	0.87[AFR][1000 genomes]
rs3940822	0.87[AFR][1000 genomes]
rs4429624	0.87[AFR][1000 genomes]
rs4688703	0.87[AFR][1000 genomes]
rs5000953	0.87[AFR][1000 genomes]
rs55833676	1.00[AMR][1000 genomes]
rs56120139	1.00[AMR][1000 genomes]
rs56737163	1.00[AMR][1000 genomes]
rs56837922	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57791592	1.00[AMR][1000 genomes]
rs59769351	1.00[AMR][1000 genomes]
rs59909173	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59949730	0.87[AFR][1000 genomes]
rs61549968	0.87[AFR][1000 genomes]
rs6446215	0.87[AFR][1000 genomes]
rs66472954	0.82[AFR][1000 genomes]
rs66867590	0.87[AFR][1000 genomes]
rs67316637	0.87[AFR][1000 genomes]
rs67410403	0.87[AFR][1000 genomes]
rs67588094	0.87[AFR][1000 genomes]
rs67672341	0.82[AFR][1000 genomes]
rs6775012	0.87[AFR][1000 genomes]
rs67813889	0.87[AFR][1000 genomes]
rs6787521	0.87[AFR][1000 genomes]
rs6791880	0.87[AFR][1000 genomes]
rs68191286	0.87[AFR][1000 genomes]
rs71326944	0.87[AFR][1000 genomes]
rs71326945	0.82[AFR][1000 genomes]
rs71329007	0.87[AFR][1000 genomes]
rs71329008	0.82[AFR][1000 genomes]
rs71329014	0.82[AFR][1000 genomes]
rs73072418	0.87[AFR][1000 genomes]
rs73072438	0.87[AFR][1000 genomes]
rs73072442	0.87[AFR][1000 genomes]
rs73079191	0.87[AFR][1000 genomes]
rs73833888	0.87[AFR][1000 genomes]
rs73835234	1.00[AMR][1000 genomes]
rs73835506	1.00[AMR][1000 genomes]
rs73835508	1.00[AMR][1000 genomes]
rs73835540	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7629253	0.87[AFR][1000 genomes]
rs7650574	0.87[AFR][1000 genomes]
rs936405	0.87[AFR][1000 genomes]
rs936406	0.87[AFR][1000 genomes]
rs9839684	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50636000-50641600	Enhancers	Esophagus	oesophagus
2	chr3:50636400-50641600	Enhancers	Pancreas	Pancrea
3	chr3:50636600-50643600	Enhancers	Left Ventricle	heart
4	chr3:50636800-50641600	Enhancers	Gastric	stomach
5	chr3:50636800-50646000	Genic enhancers	Fetal Intestine Small	intestine
6	chr3:50638800-50647400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:50639000-50642400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:50639000-50643600	Weak transcription	Aorta	Aorta
9	chr3:50639000-50643800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:50639000-50648000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:50639200-50642200	Enhancers	Stomach Mucosa	stomach
12	chr3:50639400-50641600	Enhancers	Adipose Nuclei	Adipose
13	chr3:50639400-50642200	Weak transcription	GM12878-XiMat	blood
14	chr3:50639400-50648000	Weak transcription	Fetal Brain Female	brain
15	chr3:50639600-50642800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr3:50639600-50646800	Genic enhancers	Spleen	Spleen
17	chr3:50639600-50648000	Weak transcription	Fetal Brain Male	brain
18	chr3:50639800-50641600	Enhancers	Colonic Mucosa	Colon
19	chr3:50639800-50641800	Enhancers	K562	blood
20	chr3:50639800-50642800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr3:50639800-50644200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:50639800-50644800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:50639800-50648000	Weak transcription	HUVEC	blood vessel
24	chr3:50639800-50648200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:50639800-50648200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:50639800-50648200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:50640000-50641800	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr3:50640000-50642200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:50640000-50642200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:50640000-50643200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:50640000-50644200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:50640000-50644600	Weak transcription	Thymus	Thymus
33	chr3:50640000-50647000	Genic enhancers	Fetal Muscle Leg	muscle
34	chr3:50640000-50648000	Weak transcription	Brain Substantia Nigra	brain
35	chr3:50640000-50648200	Weak transcription	NH-A	brain
36	chr3:50640200-50641600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:50640200-50641800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:50640200-50642000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:50640200-50642000	Enhancers	HepG2	liver
40	chr3:50640200-50642400	Genic enhancers	Primary T cells from cord blood	blood
41	chr3:50640200-50642400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr3:50640200-50642600	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr3:50640200-50642800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:50640200-50643800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:50640200-50644200	Weak transcription	NHLF	lung
46	chr3:50640200-50646200	Enhancers	Fetal Heart	heart
47	chr3:50640200-50647600	Weak transcription	Brain Anterior Caudate	brain
48	chr3:50640200-50647600	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr3:50640400-50641600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:50640400-50641600	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links