Variant report

Variant	rs28678122
Chromosome Location	chr15:56956314-56956315
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56954012..56957476-chr15:56973562..56976021,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10518858	0.86[EUR][1000 genomes]
rs11071282	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11071283	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11634704	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11635201	0.91[ASN][1000 genomes]
rs12148781	0.87[EUR][1000 genomes]
rs12441674	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1600830	0.84[EUR][1000 genomes]
rs1680488	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[ASN][1000 genomes]
rs2128172	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28374324	0.88[EUR][1000 genomes]
rs28379958	0.87[EUR][1000 genomes]
rs28409651	0.89[EUR][1000 genomes]
rs28441487	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28620046	0.88[ASN][1000 genomes]
rs28778716	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28782544	0.88[EUR][1000 genomes]
rs28805712	0.88[EUR][1000 genomes]
rs28813195	0.88[EUR][1000 genomes]
rs28830569	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28842489	0.87[EUR][1000 genomes]
rs28893316	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774870	0.88[EUR][1000 genomes]
rs4774876	0.88[EUR][1000 genomes]
rs4774881	0.95[EUR][1000 genomes]
rs4774891	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs534005	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[ASN][1000 genomes]
rs56327619	0.86[EUR][1000 genomes]
rs7164084	0.82[YRI][hapmap]
rs7182346	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[YRI][hapmap]
rs72744954	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72744977	0.82[ASN][1000 genomes]
rs8026706	0.88[EUR][1000 genomes]
rs8031549	0.88[EUR][1000 genomes]
rs8031966	1.00[ASW][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[ASN][1000 genomes]
rs8032893	0.88[EUR][1000 genomes]
rs809459	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[ASN][1000 genomes]
rs9806469	0.88[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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1041239	chr15:56888945-56959028	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56912800-56957000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
3	chr15:56917600-56957000	Weak transcription	Brain Anterior Caudate	brain
4	chr15:56917800-56956800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:56917800-56959800	Weak transcription	Brain Angular Gyrus	brain
6	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:56917800-56990600	Weak transcription	NHLF	lung
8	chr15:56918400-56957200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
10	chr15:56922000-56958000	Weak transcription	Lung	lung
11	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:56924000-56990800	Weak transcription	NHEK	skin
13	chr15:56924600-56957200	Weak transcription	HUVEC	blood vessel
14	chr15:56928400-56996800	Weak transcription	Gastric	stomach
15	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
16	chr15:56938600-56968200	Weak transcription	HMEC	breast
17	chr15:56939200-56990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:56939400-56986000	Weak transcription	Brain Substantia Nigra	brain
19	chr15:56941400-56960200	Weak transcription	Spleen	Spleen
20	chr15:56943600-56958000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:56944200-56959600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:56944400-56957600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:56944600-56964600	Weak transcription	K562	blood
24	chr15:56944800-56960800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:56944800-56962800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:56945200-56963200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:56945800-56963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:56945800-56990800	Weak transcription	Fetal Brain Male	brain
29	chr15:56946000-56957800	Weak transcription	Fetal Intestine Small	intestine
30	chr15:56946000-56990800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:56946200-56957400	Weak transcription	GM12878-XiMat	blood
32	chr15:56946200-56971000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:56946200-56990800	Weak transcription	Right Ventricle	heart
34	chr15:56947000-56960200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:56947200-56957000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr15:56948200-56961400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:56950200-56969200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr15:56950400-56957000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:56950400-56965000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:56950600-56956400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:56950600-56957000	Weak transcription	HSMM	muscle
42	chr15:56950600-56967200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:56951000-56956600	Weak transcription	Brain Germinal Matrix	brain
44	chr15:56951800-56960800	Strong transcription	Adipose Nuclei	Adipose
45	chr15:56952400-56960800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:56952800-56960800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:56953000-56958600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr15:56953000-56960800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:56953200-56959000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:56953200-56959800	Strong transcription	Liver	Liver

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