Variant report

Variant	rs4924660
Chromosome Location	chr15:42603708-42603709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42565275..42567071-chr15:42601912..42604080,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214013	Chromatin interaction
ENSG00000103978	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1062038	0.81[EUR][1000 genomes]
rs10775126	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851407	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10851408	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10851409	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070370	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139100	0.81[EUR][1000 genomes]
rs11631917	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631983	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638784	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438369	0.83[EUR][1000 genomes]
rs12438562	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12441642	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12441700	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594162	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12917101	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359003	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1359004	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1619030	0.85[EUR][1000 genomes]
rs1659212	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1659213	0.94[ASN][1000 genomes]
rs1659217	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1659218	0.94[ASN][1000 genomes]
rs1659219	0.94[ASN][1000 genomes]
rs1659221	0.94[ASN][1000 genomes]
rs1659222	0.94[ASN][1000 genomes]
rs1678984	0.94[ASN][1000 genomes]
rs1678985	0.86[EUR][1000 genomes]
rs1678986	0.85[EUR][1000 genomes]
rs1678991	0.87[EUR][1000 genomes]
rs1678992	0.95[ASN][1000 genomes]
rs1678993	0.95[ASN][1000 genomes]
rs1679002	0.88[EUR][1000 genomes]
rs1679009	0.85[EUR][1000 genomes]
rs1679010	0.85[EUR][1000 genomes]
rs1703750	0.88[EUR][1000 genomes]
rs1703755	0.84[EUR][1000 genomes]
rs1712418	0.87[EUR][1000 genomes]
rs1712421	0.87[EUR][1000 genomes]
rs2138831	0.85[EUR][1000 genomes]
rs2289295	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407707	0.85[EUR][1000 genomes]
rs2412682	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412685	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412705	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28364388	0.84[EUR][1000 genomes]
rs28364390	0.83[EUR][1000 genomes]
rs28364416	0.80[ASN][1000 genomes]
rs2918459	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918460	0.94[ASN][1000 genomes]
rs2918461	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743006	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3850774	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4329897	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923940	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923943	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924645	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924648	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924653	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924658	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924674	0.91[EUR][1000 genomes]
rs56702977	0.84[EUR][1000 genomes]
rs57002846	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57347762	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58313689	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59132828	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs598360	0.88[EUR][1000 genomes]
rs622442	0.85[EUR][1000 genomes]
rs633934	0.85[EUR][1000 genomes]
rs6493027	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493045	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs660126	0.89[EUR][1000 genomes]
rs677878	0.84[EUR][1000 genomes]
rs7086	0.80[EUR][1000 genomes]
rs7166785	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7168709	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7175863	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7177120	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181742	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7183015	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7183546	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73400993	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs751572	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs765830	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024732	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025601	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8026198	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8031315	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036046	0.89[EUR][1000 genomes]
rs8036187	0.89[EUR][1000 genomes]
rs8036380	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036596	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037020	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672382	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920921	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr15:42567200-42623600	Weak transcription	Fetal Brain Male	brain
2	chr15:42568400-42604600	Weak transcription	NH-A	brain
3	chr15:42568400-42656000	Weak transcription	Small Intestine	intestine
4	chr15:42568600-42630800	Weak transcription	Dnd41	blood
5	chr15:42573400-42635800	Weak transcription	Gastric	stomach
6	chr15:42573800-42605600	Weak transcription	Pancreas	Pancrea
7	chr15:42576200-42605800	Weak transcription	Esophagus	oesophagus
8	chr15:42576400-42620800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42577800-42616200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:42582000-42613400	Weak transcription	HUVEC	blood vessel
11	chr15:42585400-42623600	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:42585600-42604400	Weak transcription	Fetal Kidney	kidney
13	chr15:42585600-42607600	Weak transcription	NHLF	lung
14	chr15:42586200-42613800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr15:42593800-42616000	Weak transcription	Hela-S3	cervix
16	chr15:42596600-42604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:42596800-42609800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:42596800-42625200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:42597000-42614600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:42597800-42621200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:42598600-42604400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr15:42598600-42604600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr15:42598600-42606000	Strong transcription	Liver	Liver
24	chr15:42598600-42606600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:42598600-42606600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:42598600-42606800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:42598600-42607000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:42598600-42607600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:42598600-42607800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:42598600-42608200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr15:42598600-42610600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:42598800-42604200	Strong transcription	Primary B cells from cord blood	blood
33	chr15:42598800-42604200	Strong transcription	Brain Hippocampus Middle	brain
34	chr15:42598800-42604800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:42598800-42605000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:42598800-42605200	Strong transcription	Adipose Nuclei	Adipose
37	chr15:42598800-42605800	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:42598800-42606600	Strong transcription	Ovary	ovary
39	chr15:42599000-42604000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr15:42599000-42604200	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:42599000-42604400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr15:42599000-42604800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:42599000-42604800	Strong transcription	Aorta	Aorta
44	chr15:42599000-42604800	Strong transcription	Fetal Muscle Leg	muscle
45	chr15:42599000-42606000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr15:42599000-42606200	Strong transcription	Lung	lung
47	chr15:42599000-42606200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:42599000-42606600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:42599000-42606600	Strong transcription	Left Ventricle	heart
50	chr15:42599000-42607000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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