Variant report

Variant	rs9850471
Chromosome Location	chr3:52492475-52492476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52491058-52492925	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
2	chr2:143701599..143702362-chr3:52492018..52492705,2	MCF-7	breast:
3	chr3:52487901..52490154-chr3:52491189..52493164,2	K562	blood:

Variant related genes	Relation type
TNNC1	TF binding region
NISCH	TF binding region
ENSG00000114854	Chromatin interaction
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1011062	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011064	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035002	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1035003	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865972	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11721286	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123598	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs123603	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13065677	0.87[AMR][1000 genomes]
rs13071708	0.87[AMR][1000 genomes]
rs13074649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076508	0.87[AMR][1000 genomes]
rs13089892	0.87[AMR][1000 genomes]
rs13091360	0.87[AMR][1000 genomes]
rs13093555	0.82[AMR][1000 genomes]
rs13096571	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13098856	0.87[AMR][1000 genomes]
rs1541495	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs164636	0.82[AMR][1000 genomes]
rs164637	0.82[AMR][1000 genomes]
rs2109557	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109558	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109559	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2215466	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335928	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335929	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34181173	0.87[AMR][1000 genomes]
rs34332947	0.87[AMR][1000 genomes]
rs34385735	0.82[AMR][1000 genomes]
rs34551211	0.82[AMR][1000 genomes]
rs34628357	0.87[AMR][1000 genomes]
rs34827613	0.91[AMR][1000 genomes]
rs35130772	0.87[AMR][1000 genomes]
rs353545	0.82[AMR][1000 genomes]
rs3755810	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796342	0.87[AMR][1000 genomes]
rs409803	0.81[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs419050	0.91[AMR][1000 genomes]
rs419604	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs419752	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4312651	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4687544	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687614	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687616	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687617	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687618	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687621	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs575476	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs613519	0.81[EUR][1000 genomes]
rs6414568	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445483	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445484	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445485	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787493	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795333	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6810027	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297396	0.87[AMR][1000 genomes]
rs728408	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs758800	1.00[EUR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs887514	0.93[EUR][1000 genomes]
rs929528	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929529	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968588	0.85[AMR][1000 genomes]
rs9846089	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847332	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv876794	chr3:52485876-52496229	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52490200-52492600	Flanking Active TSS	HMEC	breast
2	chr3:52490800-52492800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52490800-52492800	Weak transcription	Aorta	Aorta
4	chr3:52490800-52499200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:52491000-52492800	Weak transcription	Pancreas	Pancrea
6	chr3:52491000-52493200	Genic enhancers	Fetal Thymus	thymus
7	chr3:52491200-52492600	Genic enhancers	Brain Cingulate Gyrus	brain
8	chr3:52491200-52492800	Weak transcription	Colonic Mucosa	Colon
9	chr3:52491200-52493000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:52491200-52493200	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr3:52491200-52493400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:52491200-52493600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:52491200-52498800	Strong transcription	Primary T cells from cord blood	blood
14	chr3:52491400-52495400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:52491400-52497200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:52491400-52500000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:52491400-52501600	Weak transcription	Right Atrium	heart
18	chr3:52491400-52502200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:52491600-52492600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:52491600-52492800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:52491600-52493600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr3:52491600-52493600	Strong transcription	NHLF	lung
23	chr3:52491600-52493800	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr3:52491600-52495400	Strong transcription	Fetal Lung	lung
25	chr3:52491600-52496800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:52491600-52499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:52491600-52500000	Strong transcription	Fetal Intestine Large	intestine
28	chr3:52491600-52500600	Strong transcription	Fetal Intestine Small	intestine
29	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
30	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
31	chr3:52491800-52492600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:52491800-52492600	Genic enhancers	Fetal Brain Female	brain
33	chr3:52491800-52492600	Weak transcription	Gastric	stomach
34	chr3:52491800-52492600	Genic enhancers	Monocytes-CD14+_RO01746	blood
35	chr3:52491800-52492800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:52491800-52492800	Weak transcription	Brain Angular Gyrus	brain
37	chr3:52491800-52492800	Genic enhancers	Brain Germinal Matrix	brain
38	chr3:52491800-52492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:52491800-52493000	Weak transcription	Fetal Brain Male	brain
40	chr3:52491800-52493000	Genic enhancers	Dnd41	blood
41	chr3:52491800-52493200	Strong transcription	Primary B cells from cord blood	blood
42	chr3:52491800-52493400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
43	chr3:52491800-52493400	Strong transcription	Hela-S3	cervix
44	chr3:52491800-52493400	Strong transcription	HSMM	muscle
45	chr3:52491800-52493600	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr3:52491800-52493600	Strong transcription	NH-A	brain
47	chr3:52491800-52493800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:52491800-52493800	Strong transcription	Right Ventricle	heart
49	chr3:52491800-52493800	Strong transcription	HepG2	liver
50	chr3:52491800-52494000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links