Variant report

Variant	rs28620278
Chromosome Location	chr15:56959028-56959029
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	chr15:56957841..56960348-chr15:57024412..57027356,2	MCF-7	breast:
2	chr15:56947710..56949371-chr15:56958566..56961070,2	K562	blood:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10152127	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10518870	0.88[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs11071280	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11071287	0.87[AMR][1000 genomes]
rs11630168	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11633363	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11635333	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636994	0.91[ASN][1000 genomes]
rs11638497	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638580	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11638707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11852277	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11856558	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11857388	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857706	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12148500	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12442189	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12591502	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12592389	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595822	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12898521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12898760	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12900244	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12900441	0.81[EUR][1000 genomes]
rs12901887	0.82[CEU][hapmap]
rs12903283	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12903336	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903862	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12905514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12906591	0.81[EUR][1000 genomes]
rs12906830	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12908906	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910442	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910459	0.89[CEU][hapmap]
rs12911191	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12911381	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912666	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs12913361	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12913871	0.81[EUR][1000 genomes]
rs12913960	0.81[EUR][1000 genomes]
rs12916079	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1424694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16977020	0.90[CHB][hapmap]
rs17238845	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1979467	0.87[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1994081	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2170459	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2170463	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279298	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279299	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2414480	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28480089	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784554	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3803457	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816752	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs3929265	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4774884	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4774886	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs521904	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs538382	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs553421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493885	0.81[EUR][1000 genomes]
rs7162317	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7168178	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap]
rs7174432	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178796	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7182187	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs795032	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8025391	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8036217	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8041540	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8043223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.96[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	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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
2	chr15:56917800-56959800	Weak transcription	Brain Angular Gyrus	brain
3	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:56917800-56990600	Weak transcription	NHLF	lung
5	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
6	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:56924000-56990800	Weak transcription	NHEK	skin
8	chr15:56928400-56996800	Weak transcription	Gastric	stomach
9	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
10	chr15:56938600-56968200	Weak transcription	HMEC	breast
11	chr15:56939200-56990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:56939400-56986000	Weak transcription	Brain Substantia Nigra	brain
13	chr15:56941400-56960200	Weak transcription	Spleen	Spleen
14	chr15:56944200-56959600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:56944600-56964600	Weak transcription	K562	blood
16	chr15:56944800-56960800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:56944800-56962800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:56945200-56963200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr15:56945800-56963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:56945800-56990800	Weak transcription	Fetal Brain Male	brain
21	chr15:56946000-56990800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:56946200-56971000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:56946200-56990800	Weak transcription	Right Ventricle	heart
24	chr15:56947000-56960200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:56948200-56961400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:56950200-56969200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:56950400-56965000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:56950600-56967200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:56951800-56960800	Strong transcription	Adipose Nuclei	Adipose
30	chr15:56952400-56960800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:56952800-56960800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:56953000-56960800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:56953200-56959800	Strong transcription	Liver	Liver
34	chr15:56953200-56961600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:56953800-56960000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:56954000-56959200	Strong transcription	Placenta	Placenta
37	chr15:56954000-56968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:56954200-56965200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:56954400-56960400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:56954400-56960600	Strong transcription	Osteobl	bone
41	chr15:56954600-56960400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr15:56954800-56959200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:56954800-56959400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:56954800-56959400	Strong transcription	Fetal Intestine Large	intestine
45	chr15:56954800-56969400	Strong transcription	Fetal Thymus	thymus
46	chr15:56955000-56959400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:56955000-56959400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:56955000-56960800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:56955000-56961200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:56955000-56961400	Strong transcription	Primary monocytes fromperipheralblood	blood

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