Variant report

Variant	rs8001089
Chromosome Location	chr13:79956541-79956542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:79955549..79959842-chr13:79960157..79964525,5	K562	blood:
2	chr13:79955154..79956833-chr13:79959758..79961618,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252496	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1324872	1.00[AMR][1000 genomes]
rs1328043	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1328044	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1328045	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1335376	1.00[AMR][1000 genomes]
rs1359411	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1408655	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1410330	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1410331	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1410333	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1555731	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1571322	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1590466	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1749987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1752645	0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1853721	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1856995	1.00[AMR][1000 genomes]
rs1885817	1.00[AMR][1000 genomes]
rs1980882	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2147567	1.00[AMR][1000 genomes]
rs2265032	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2484341	1.00[AMR][1000 genomes]
rs2484342	1.00[AMR][1000 genomes]
rs2760109	1.00[AMR][1000 genomes]
rs2760110	1.00[AMR][1000 genomes]
rs2765081	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2783128	1.00[AMR][1000 genomes]
rs2991462	1.00[AMR][1000 genomes]
rs314691	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs314696	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs314697	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs314698	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs314699	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3861140	1.00[ASN][1000 genomes]
rs4052508	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs418177	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4300513	1.00[AMR][1000 genomes]
rs450755	1.00[AMR][1000 genomes]
rs4884128	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4885630	1.00[AMR][1000 genomes]
rs6563092	1.00[AMR][1000 genomes]
rs6563099	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6563101	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563102	1.00[AMR][1000 genomes]
rs6563103	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563108	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563118	1.00[AMR][1000 genomes]
rs7317607	1.00[YRI][hapmap]
rs7317825	1.00[YRI][hapmap]
rs7324585	1.00[AMR][1000 genomes]
rs7324725	1.00[YRI][hapmap]
rs7325232	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7325772	1.00[YRI][hapmap]
rs7326625	1.00[ASN][1000 genomes]
rs7328114	1.00[YRI][hapmap]
rs7329123	1.00[YRI][hapmap]
rs7331575	1.00[YRI][hapmap]
rs7333101	1.00[YRI][hapmap]
rs7333651	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7334029	1.00[AMR][1000 genomes]
rs7334978	1.00[ASN][1000 genomes]
rs73566469	1.00[ASN][1000 genomes]
rs7981807	1.00[YRI][hapmap]
rs7983606	1.00[YRI][hapmap]
rs7983730	1.00[YRI][hapmap]
rs7984241	1.00[YRI][hapmap]
rs7993115	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7993478	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7994560	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7996740	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7996869	1.00[AMR][1000 genomes]
rs7998224	1.00[AMR][1000 genomes]
rs8001822	1.00[AMR][1000 genomes]
rs927696	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9318630	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9318631	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9318637	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9530903	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545056	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9545084	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9545096	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545102	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545105	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545107	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9545111	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9601212	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][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	nsv900586	chr13:79892722-79968467	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv900587	chr13:79894736-79956691	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:79893200-79957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:79941800-79956600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr13:79942000-79967400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:79943000-79957800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:79946000-79960000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:79946400-79969200	Weak transcription	Fetal Kidney	kidney
7	chr13:79951200-79959800	Weak transcription	Fetal Heart	heart
8	chr13:79951200-79962200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:79951200-79979200	Weak transcription	Esophagus	oesophagus
10	chr13:79951400-79956600	Weak transcription	Brain Substantia Nigra	brain
11	chr13:79951400-79956600	Weak transcription	Colon Smooth Muscle	Colon
12	chr13:79951400-79956600	Weak transcription	Small Intestine	intestine
13	chr13:79951400-79956600	Weak transcription	HSMMtube	muscle
14	chr13:79951400-79956800	Weak transcription	A549	lung
15	chr13:79951400-79957200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:79951400-79959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr13:79951400-79960000	Weak transcription	NHDF-Ad	bronchial
18	chr13:79951400-79962200	Weak transcription	Lung	lung
19	chr13:79951600-79956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr13:79951600-79960000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr13:79951600-79960000	Weak transcription	NH-A	brain
22	chr13:79951600-79965400	Weak transcription	Brain Angular Gyrus	brain
23	chr13:79951600-79969000	Weak transcription	Fetal Brain Male	brain
24	chr13:79951800-79956600	Weak transcription	NHEK	skin
25	chr13:79951800-79960000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr13:79951800-79961800	Weak transcription	Brain Germinal Matrix	brain
27	chr13:79951800-79978200	Weak transcription	Aorta	Aorta
28	chr13:79952000-79967200	Weak transcription	Brain Hippocampus Middle	brain
29	chr13:79952000-79967600	Weak transcription	Gastric	stomach
30	chr13:79952200-79956800	Weak transcription	Stomach Mucosa	stomach
31	chr13:79952200-79960000	Weak transcription	Ovary	ovary
32	chr13:79952200-79967600	Weak transcription	Pancreas	Pancrea
33	chr13:79952200-79967600	Weak transcription	Spleen	Spleen
34	chr13:79952400-79956600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr13:79952400-79956600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr13:79952400-79956600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr13:79952400-79956600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr13:79952400-79956600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:79952400-79956600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr13:79952400-79956800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr13:79952400-79956800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr13:79952400-79956800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr13:79952400-79957600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr13:79952400-79958000	Weak transcription	HepG2	liver
45	chr13:79952400-79960000	Weak transcription	NHLF	lung
46	chr13:79952400-79960000	Weak transcription	Osteobl	bone
47	chr13:79952400-79962200	Weak transcription	Psoas Muscle	Psoas
48	chr13:79952400-79963000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr13:79952400-79963600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr13:79952400-79966800	Weak transcription	Thymus	Thymus

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