Variant report

Variant	rs12439583
Chromosome Location	chr15:79201108-79201109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:79200123..79202028-chr15:79275613..79277156,2	MCF-7	breast:
2	chr15:79200824..79204209-chr15:79206571..79210953,6	K562	blood:
3	chr15:79165877..79167855-chr15:79198881..79201176,2	MCF-7	breast:
4	chr15:79198644..79201340-chr15:79270795..79273687,2	K562	blood:
5	chr15:79200824..79204913-chr15:79206571..79210692,6	K562	blood:
6	chr15:79200401..79202827-chr15:79229595..79232492,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177699	Chromatin interaction
ENSG00000103811	Chromatin interaction
ENSG00000058335	Chromatin interaction
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10444811	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857042	1.00[EUR][1000 genomes]
rs12050510	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050636	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12438191	0.99[EUR][1000 genomes]
rs12438433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440205	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12440662	0.85[ASN][1000 genomes]
rs12442152	0.91[ASN][1000 genomes]
rs12443105	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592618	0.88[EUR][1000 genomes]
rs1435163	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16970194	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16970223	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs16970227	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16970233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970244	1.00[EUR][1000 genomes]
rs1836556	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289691	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34866535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622479	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4624135	0.88[EUR][1000 genomes]
rs4628930	0.84[ASN][1000 genomes]
rs4778909	0.84[CEU][hapmap]
rs56031815	0.80[ASN][1000 genomes]
rs56272008	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56281795	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56343754	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56687292	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58848937	1.00[EUR][1000 genomes]
rs59312571	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59735519	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60634495	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61157089	0.91[ASN][1000 genomes]
rs62011029	0.84[ASN][1000 genomes]
rs62011032	0.84[ASN][1000 genomes]
rs62011033	0.84[ASN][1000 genomes]
rs62011034	0.84[ASN][1000 genomes]
rs62011036	0.88[ASN][1000 genomes]
rs62011050	0.91[ASN][1000 genomes]
rs62011052	0.90[ASN][1000 genomes]
rs62011055	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62011056	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62013160	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62013184	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62013185	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62013186	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013191	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62013193	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62013196	0.99[EUR][1000 genomes]
rs6495343	0.84[ASN][1000 genomes]
rs6495351	0.87[AFR][1000 genomes]
rs7171539	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7174727	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs7179763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7181240	0.85[ASN][1000 genomes]
rs7497610	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8025870	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8026077	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8027635	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028352	0.90[EUR][1000 genomes]
rs8029496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8031280	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8032867	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8035028	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8035305	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8039140	0.87[EUR][1000 genomes]
rs8039144	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8042187	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 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	chr15:79171200-79215600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:79171800-79207800	Strong transcription	Fetal Thymus	thymus
3	chr15:79172000-79202800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:79172200-79207000	Strong transcription	Primary B cells from peripheral blood	blood
5	chr15:79172400-79216200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:79172600-79201800	Strong transcription	Duodenum Mucosa	Duodenum
7	chr15:79172600-79207400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:79172800-79202600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:79172800-79205400	Strong transcription	Fetal Lung	lung
10	chr15:79172800-79206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:79173400-79203000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:79173600-79206200	Strong transcription	Fetal Muscle Leg	muscle
13	chr15:79173600-79206400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr15:79173800-79206400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr15:79176600-79202400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:79176800-79215200	Strong transcription	Dnd41	blood
17	chr15:79177000-79202200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:79177000-79207800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr15:79177200-79206800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr15:79178200-79219400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:79184000-79204600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:79185600-79208600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:79187400-79213600	Weak transcription	Small Intestine	intestine
24	chr15:79188000-79209400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:79190000-79208200	Strong transcription	Primary T cells from cord blood	blood
26	chr15:79190000-79222200	Strong transcription	Thymus	Thymus
27	chr15:79190400-79204200	Strong transcription	Fetal Stomach	stomach
28	chr15:79190400-79207000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:79190400-79208200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:79191800-79203400	Strong transcription	Brain Germinal Matrix	brain
31	chr15:79192600-79201800	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr15:79194000-79202800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:79194800-79201200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:79194800-79207000	Strong transcription	K562	blood
35	chr15:79196400-79203200	Strong transcription	Fetal Kidney	kidney
36	chr15:79197000-79202400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:79197200-79202400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:79197200-79213600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:79198200-79202000	Strong transcription	Brain Anterior Caudate	brain
40	chr15:79198400-79204400	Strong transcription	NHEK	skin
41	chr15:79198600-79202200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:79198800-79201600	Weak transcription	Gastric	stomach
43	chr15:79198800-79201600	Strong transcription	Ovary	ovary
44	chr15:79198800-79201800	Strong transcription	Spleen	Spleen
45	chr15:79198800-79202000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:79198800-79202800	Strong transcription	Aorta	Aorta
47	chr15:79199000-79201800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr15:79199000-79206200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:79199000-79206400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:79199000-79213800	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links