Variant report

Variant	rs3924029
Chromosome Location	chr2:64101569-64101570
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:63814371..63817295-chr2:64100635..64103501,2	MCF-7	breast:
2	chr2:64097542..64099812-chr2:64100980..64103347,2	MCF-7	breast:
3	chr2:64100029..64102648-chr2:64113034..64115092,3	K562	blood:
4	chr2:64101527..64104952-chr2:64106115..64108831,3	MCF-7	breast:
5	chr2:64100029..64102701-chr2:64113484..64115928,2	K562	blood:
6	chr2:64095211..64099085-chr2:64100038..64104293,5	K562	blood:
7	chr2:64066124..64069765-chr2:64101066..64104026,3	K562	blood:

Variant related genes	Relation type
ENSG00000169764	Chromatin interaction
ENSG00000143951	Chromatin interaction
ENSG00000014641	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10496104	0.81[EUR][1000 genomes]
rs11896894	0.81[EUR][1000 genomes]
rs13431437	1.00[ASN][1000 genomes]
rs17028099	1.00[ASN][1000 genomes]
rs17028239	0.81[EUR][1000 genomes]
rs17554748	1.00[ASN][1000 genomes]
rs28838707	1.00[ASN][1000 genomes]
rs4277507	0.81[EUR][1000 genomes]
rs4470330	0.81[EUR][1000 genomes]
rs55748575	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56342040	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57085982	0.81[EUR][1000 genomes]
rs57120200	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57329063	1.00[ASN][1000 genomes]
rs57844293	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57877849	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58208651	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58422338	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58472560	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58495096	1.00[ASN][1000 genomes]
rs59335889	0.81[EUR][1000 genomes]
rs59540641	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136361	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136362	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62136364	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136366	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136367	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136369	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136391	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136393	1.00[EUR][1000 genomes]
rs62136397	1.00[EUR][1000 genomes]
rs62136398	0.81[EUR][1000 genomes]
rs62136400	1.00[EUR][1000 genomes]
rs62136402	1.00[EUR][1000 genomes]
rs62136407	0.81[EUR][1000 genomes]
rs62136423	0.81[EUR][1000 genomes]
rs62138760	1.00[ASN][1000 genomes]
rs62138819	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138820	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138822	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138823	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138824	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745518	1.00[ASN][1000 genomes]
rs6751397	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73937260	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73937264	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73937268	1.00[ASN][1000 genomes]
rs7558570	0.91[EUR][1000 genomes]
rs7582457	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601187	1.00[ASN][1000 genomes]
rs7606341	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 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	chr2:64070200-64103000	Weak transcription	Gastric	stomach
2	chr2:64078000-64108000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:64082200-64110000	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:64083000-64123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:64083000-64129200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:64083200-64110200	Weak transcription	Small Intestine	intestine
7	chr2:64083200-64110600	Weak transcription	Pancreas	Pancrea
8	chr2:64085600-64102400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:64086600-64110000	Weak transcription	Esophagus	oesophagus
10	chr2:64086800-64102800	Weak transcription	Right Ventricle	heart
11	chr2:64087600-64101800	Genic enhancers	Liver	Liver
12	chr2:64088000-64107800	Weak transcription	Colonic Mucosa	Colon
13	chr2:64090000-64102000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:64090600-64102800	Weak transcription	Stomach Mucosa	stomach
15	chr2:64091400-64110000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:64091800-64107800	Weak transcription	Brain Germinal Matrix	brain
17	chr2:64093000-64106400	Strong transcription	Fetal Thymus	thymus
18	chr2:64093800-64107600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:64093800-64109200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:64093800-64110000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:64094000-64102400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:64094000-64102800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:64094000-64107800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:64094000-64109400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:64094000-64110800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:64095400-64102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:64096200-64103400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
28	chr2:64097600-64102000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:64098200-64102800	Weak transcription	Right Atrium	heart
30	chr2:64098400-64101800	Enhancers	Aorta	Aorta
31	chr2:64098600-64102200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:64098600-64102800	Weak transcription	Lung	lung
33	chr2:64098600-64106000	Strong transcription	Primary T cells from cord blood	blood
34	chr2:64098800-64101600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:64099000-64102400	Strong transcription	Hela-S3	cervix
36	chr2:64099000-64102800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:64099000-64103200	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr2:64099000-64105800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:64099200-64101800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:64099200-64102000	ZNF genes & repeats	GM12878-XiMat	blood
41	chr2:64099200-64103000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr2:64099200-64103000	Strong transcription	Thymus	Thymus
43	chr2:64099400-64101600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:64099400-64103200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:64099400-64103400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:64099400-64106200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:64099600-64105400	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr2:64099800-64101800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:64099800-64101800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:64099800-64101800	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links