Variant report

Variant	rs334065
Chromosome Location	chr2:179002468-179002469
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	chr2:179001004-179003397	K562	blood:	n/a	n/a
2	POLR2A	chr2:179001969-179003414	K562	blood:	n/a	n/a
3	CTCF	chr2:179002460-179002710	HCM	heart:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:179001333..179003104-chr2:179278827..179280728,2	MCF-7	breast:
2	chr2:178998158..179000091-chr2:179001062..179003808,2	K562	blood:
3	chr2:178993079..178995697-chr2:179002423..179004658,2	K562	blood:

Variant related genes	Relation type
RNU5E-9P	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12987593	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12989423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989778	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013828	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs13033194	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419755	1.00[ASN][1000 genomes]
rs334055	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334060	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334071	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334073	0.85[AFR][1000 genomes]
rs334076	1.00[ASN][1000 genomes]
rs334077	1.00[ASN][1000 genomes]
rs34069002	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34395717	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34702539	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34927879	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35620189	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35938761	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737266	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423553	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423554	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423555	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178978000-179003200	Weak transcription	Spleen	Spleen
2	chr2:178978000-179003800	Weak transcription	Aorta	Aorta
3	chr2:178978000-179016400	Weak transcription	Gastric	stomach
4	chr2:178978200-179002800	Weak transcription	Fetal Stomach	stomach
5	chr2:178978600-179003000	Weak transcription	Right Ventricle	heart
6	chr2:178978600-179003600	Weak transcription	Fetal Heart	heart
7	chr2:178978800-179004000	Weak transcription	Brain Germinal Matrix	brain
8	chr2:178979000-179005400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:178987200-179005800	Weak transcription	Psoas Muscle	Psoas
10	chr2:178987400-179002800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:178987800-179017000	Weak transcription	Fetal Lung	lung
12	chr2:178988600-179002800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:178990200-179007000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:178990400-179003000	Weak transcription	HMEC	breast
15	chr2:178990800-179003800	Weak transcription	GM12878-XiMat	blood
16	chr2:178991000-179009600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:178991200-179007400	Weak transcription	Osteobl	bone
18	chr2:178991800-179003600	Weak transcription	Left Ventricle	heart
19	chr2:178992200-179003000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:178992400-179003200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:178992400-179007800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:178993200-179016800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:178993400-179002800	Weak transcription	Fetal Brain Female	brain
24	chr2:178994400-179003000	Weak transcription	Fetal Intestine Large	intestine
25	chr2:178994400-179003600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:178994400-179007200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:178994400-179007200	Weak transcription	HSMMtube	muscle
28	chr2:178994600-179002600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:178994600-179002600	Weak transcription	NH-A	brain
30	chr2:178994600-179004000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:178994600-179004200	Weak transcription	Brain Anterior Caudate	brain
32	chr2:178994600-179005800	Weak transcription	Liver	Liver
33	chr2:178994600-179007000	Weak transcription	Fetal Kidney	kidney
34	chr2:178995400-179003400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:178995800-179003600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:178997800-179006800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:178997800-179008200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:178998600-179002600	Strong transcription	Primary T cells from cord blood	blood
39	chr2:178999600-179004200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:178999800-179003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:179000000-179002800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:179000200-179002800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:179000200-179003800	Weak transcription	Dnd41	blood
44	chr2:179000200-179006000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:179000200-179007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:179000400-179003600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:179000400-179004000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:179000400-179005600	Weak transcription	A549	lung
49	chr2:179000400-179007200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:179000600-179004800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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