Variant report

Variant	rs6662463
Chromosome Location	chr1:151871309-151871310
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151871030..151873827-chr1:151880449..151882016,2	K562	blood:
2	chr1:151869400..151872007-chr1:151876004..151878841,3	K562	blood:
3	chr1:151861522..151872673-chr1:151876647..151885029,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1003107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158030	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1038746	0.82[AFR][1000 genomes]
rs1038748	0.82[AFR][1000 genomes]
rs1048910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749666	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10788813	0.86[EUR][1000 genomes]
rs10788814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788816	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888448	0.85[AMR][1000 genomes]
rs10888449	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888450	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10888451	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10888453	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204905	0.95[AMR][1000 genomes]
rs11204911	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11204912	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1352654	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1387834	0.82[AFR][1000 genomes]
rs1473493	0.82[AFR][1000 genomes]
rs1473494	0.82[AFR][1000 genomes]
rs1473495	0.82[AFR][1000 genomes]
rs1490187	0.90[EUR][1000 genomes]
rs1490190	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1552605	0.82[AFR][1000 genomes]
rs1552606	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1552607	0.82[AFR][1000 genomes]
rs1602245	0.82[AFR][1000 genomes]
rs17583707	0.85[ASN][1000 genomes]
rs1826170	0.82[AFR][1000 genomes]
rs1826171	0.82[AFR][1000 genomes]
rs1844542	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1873310	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1873311	0.82[AFR][1000 genomes]
rs1873312	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054948	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087549	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2130526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171917	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2338018	0.82[AFR][1000 genomes]
rs2338200	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2338203	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2338204	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338210	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2932563	0.82[AFR][1000 genomes]
rs2932578	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932588	0.82[AFR][1000 genomes]
rs2932591	0.82[AFR][1000 genomes]
rs2932592	0.82[AFR][1000 genomes]
rs2932595	0.82[AFR][1000 genomes]
rs2932596	0.82[AFR][1000 genomes]
rs2932597	0.82[AFR][1000 genomes]
rs2999514	0.82[AFR][1000 genomes]
rs2999518	0.82[AFR][1000 genomes]
rs2999520	0.82[AFR][1000 genomes]
rs2999524	0.82[AFR][1000 genomes]
rs2999525	0.82[AFR][1000 genomes]
rs2999527	0.82[AFR][1000 genomes]
rs2999529	0.82[AFR][1000 genomes]
rs2999558	0.82[AFR][1000 genomes]
rs3007682	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3007699	0.82[AFR][1000 genomes]
rs3007700	0.82[AFR][1000 genomes]
rs3007701	0.82[AFR][1000 genomes]
rs3748805	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551598	0.88[EUR][1000 genomes]
rs4845385	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845660	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4845664	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4845699	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61113720	0.85[ASN][1000 genomes]
rs6587626	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587627	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587628	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587630	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6659029	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6678664	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6685291	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6690443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691350	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529451	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7532721	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7541498	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7544380	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7545863	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7552869	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs902314	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs902315	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs902316	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs971888	0.82[AFR][1000 genomes]
rs9943225	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6662463	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151841200-151880800	Weak transcription	NHLF	lung
3	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
4	chr1:151844800-151877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:151846400-151871600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:151854000-151880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:151857000-151873000	Weak transcription	GM12878-XiMat	blood
8	chr1:151857600-151873400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:151857600-151874200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:151860600-151871800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:151860600-151877600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:151860800-151879800	Weak transcription	Brain Angular Gyrus	brain
13	chr1:151861600-151879800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:151862400-151880400	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:151864000-151873000	Weak transcription	Fetal Heart	heart
16	chr1:151864800-151881400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:151866200-151879600	Weak transcription	NHDF-Ad	bronchial
18	chr1:151866200-151880200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:151866400-151874400	Weak transcription	Fetal Lung	lung
20	chr1:151866600-151879800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:151867200-151872800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:151867200-151879600	Weak transcription	Fetal Stomach	stomach
23	chr1:151867400-151871600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:151867400-151877600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:151867400-151877600	Weak transcription	Osteobl	bone
26	chr1:151867400-151878600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:151867600-151877200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:151867600-151877600	Weak transcription	NH-A	brain
29	chr1:151868000-151872200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:151868000-151879800	Weak transcription	Liver	Liver
31	chr1:151868000-151880200	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:151868000-151880400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:151868000-151880800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:151868400-151871400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:151868400-151871400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:151868600-151872600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:151869000-151872200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr1:151869400-151871600	Enhancers	Fetal Intestine Large	intestine
39	chr1:151869600-151871400	Enhancers	Small Intestine	intestine
40	chr1:151869600-151871800	Enhancers	Dnd41	blood
41	chr1:151869800-151871400	Enhancers	Adipose Nuclei	Adipose
42	chr1:151869800-151871800	Enhancers	Fetal Thymus	thymus
43	chr1:151870000-151871800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:151870200-151871400	Enhancers	Lung	lung
45	chr1:151870200-151871600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:151870200-151871600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:151870200-151871800	Enhancers	Fetal Intestine Small	intestine
48	chr1:151870200-151871800	Enhancers	Thymus	Thymus
49	chr1:151870400-151871400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:151870400-151871600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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