Variant report

Variant	rs6771558
Chromosome Location	chr3:52497254-52497255
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52493353..52494882-chr3:52496416..52498026,2	K562	blood:
2	chr3:52310733..52312437-chr3:52495825..52497438,2	MCF-7	breast:
3	chr3:52496100..52498800-chr3:52502914..52504460,2	K562	blood:

Variant related genes	Relation type
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[JPT][hapmap];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]
rs1077142	1.00[JPT][hapmap]
rs10865972	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123598	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap]
rs13065677	0.87[AMR][1000 genomes]
rs13071708	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs13074649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs13076890	1.00[JPT][hapmap]
rs13089892	0.87[AMR][1000 genomes]
rs13091360	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs13091545	1.00[JPT][hapmap]
rs13093555	0.82[AMR][1000 genomes]
rs13096571	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13098856	0.87[AMR][1000 genomes]
rs1541495	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs164636	0.82[AMR][1000 genomes]
rs164637	0.82[AMR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	1.00[JPT][hapmap]
rs2109557	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109558	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109559	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335640	1.00[JPT][hapmap]
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	1.00[JPT][hapmap];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]
rs34762015	1.00[JPT][hapmap]
rs34827613	0.91[AMR][1000 genomes]
rs35130772	0.87[AMR][1000 genomes]
rs353545	0.82[AMR][1000 genomes]
rs35860312	1.00[JPT][hapmap]
rs3755810	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796342	0.87[AMR][1000 genomes]
rs3796343	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs419050	1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs419604	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs419752	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4312651	1.00[JPT][hapmap];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	1.00[JPT][hapmap];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[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687618	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[JPT][hapmap];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	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs575476	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6414568	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445386	1.00[JPT][hapmap]
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[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6782162	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	1.00[JPT][hapmap];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]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[JPT][hapmap];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[JPT][hapmap];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[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap];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]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[JPT][hapmap];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]
rs9850471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52490800-52499200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52491200-52498800	Strong transcription	Primary T cells from cord blood	blood
3	chr3:52491400-52500000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:52491400-52501600	Weak transcription	Right Atrium	heart
5	chr3:52491400-52502200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:52491600-52499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:52491600-52500000	Strong transcription	Fetal Intestine Large	intestine
8	chr3:52491600-52500600	Strong transcription	Fetal Intestine Small	intestine
9	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
10	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
11	chr3:52491800-52497400	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr3:52491800-52497400	Strong transcription	Rectal Smooth Muscle	rectum
13	chr3:52491800-52498400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:52491800-52498600	Strong transcription	Liver	Liver
15	chr3:52491800-52499400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:52491800-52499400	Strong transcription	Osteobl	bone
17	chr3:52491800-52499600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:52491800-52500000	Strong transcription	Lung	lung
19	chr3:52491800-52500200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:52491800-52502400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:52491800-52502400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:52491800-52502800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:52491800-52506400	Weak transcription	Stomach Mucosa	stomach
24	chr3:52491800-52517200	Strong transcription	Fetal Stomach	stomach
25	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:52492000-52500000	Strong transcription	Placenta	Placenta
30	chr3:52492000-52500600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:52492000-52502400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:52492000-52502600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:52492000-52503400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:52492000-52516800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:52492000-52517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:52492200-52506200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:52492600-52497400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:52492600-52497400	Strong transcription	Fetal Brain Female	brain
40	chr3:52493000-52499400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:52493000-52502800	Strong transcription	Dnd41	blood
42	chr3:52493000-52506800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:52493200-52497400	Strong transcription	NHEK	skin
45	chr3:52493200-52497600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:52493200-52499400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:52493200-52500800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr3:52493200-52507000	Strong transcription	Fetal Thymus	thymus
49	chr3:52493400-52497600	Strong transcription	HMEC	breast
50	chr3:52493400-52499200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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