Variant report

Variant	rs2412416
Chromosome Location	chr15:39921759-39921760
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:39921577..39922712-chr15:39960446..39961289,4	MCF-7	breast:
2	chr15:39871401..39883645-chr15:39918779..39926575,24	MCF-7	breast:
3	chr15:39872729..39875575-chr15:39921037..39923866,5	MCF-7	breast:
4	chr15:39921577..39922481-chr15:39960668..39961289,3	MCF-7	breast:
5	chr15:39603952..39606127-chr15:39921042..39922610,2	MCF-7	breast:
6	chr15:39921354..39922952-chr3:64065874..64067555,2	MCF-7	breast:
7	chr15:39920700..39923129-chr15:39958970..39962199,4	MCF-7	breast:
8	chr15:39887137..39895767-chr15:39912868..39924962,20	MCF-7	breast:
9	chr15:39890030..39893862-chr15:39920684..39923175,4	MCF-7	breast:
10	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
11	chr15:39921225..39923942-chr15:39930395..39933053,2	MCF-7	breast:
12	chr15:39921489..39922463-chr15:39960386..39961014,2	MCF-7	breast:
13	chr15:39904208..39905755-chr15:39920256..39923195,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10520137	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10520142	0.90[ASN][1000 genomes]
rs11070220	0.80[ASN][1000 genomes]
rs11070221	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070222	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070223	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070224	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070225	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070226	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632117	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638558	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852591	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11852649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856971	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857819	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12899323	0.90[EUR][1000 genomes]
rs12901142	0.88[EUR][1000 genomes]
rs12903514	0.88[EUR][1000 genomes]
rs12908846	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12911549	0.91[EUR][1000 genomes]
rs16969386	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16969395	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16969410	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16969426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16969478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1876852	0.92[ASN][1000 genomes]
rs1876853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411299	0.90[EUR][1000 genomes]
rs2411308	0.87[EUR][1000 genomes]
rs2411309	0.88[EUR][1000 genomes]
rs2411311	0.91[EUR][1000 genomes]
rs2411313	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2411314	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2411315	0.89[ASN][1000 genomes]
rs2412412	0.91[ASN][1000 genomes]
rs2412413	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412414	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412418	0.93[ASN][1000 genomes]
rs2412419	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412420	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412421	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2631700	0.82[EUR][1000 genomes]
rs28437905	0.88[EUR][1000 genomes]
rs2898685	0.90[EUR][1000 genomes]
rs2898686	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743125	0.80[ASN][1000 genomes]
rs4319740	0.92[ASN][1000 genomes]
rs4349120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480779	0.89[EUR][1000 genomes]
rs4526992	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4547308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583211	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4606692	0.91[EUR][1000 genomes]
rs4628934	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56938133	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59449051	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60164392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60195210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61130460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61439563	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61568256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492909	0.88[EUR][1000 genomes]
rs66781090	0.91[ASN][1000 genomes]
rs67239630	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7162070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162781	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167100	0.88[EUR][1000 genomes]
rs7167184	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167366	0.82[ASN][1000 genomes]
rs7168755	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7169478	0.95[EUR][1000 genomes]
rs7169574	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7170335	0.89[ASN][1000 genomes]
rs7176721	0.89[ASN][1000 genomes]
rs7177324	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7179608	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7180675	0.89[ASN][1000 genomes]
rs72725079	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72725080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72725084	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72725093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72725101	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8032035	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8032289	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033902	0.88[EUR][1000 genomes]
rs8034885	0.85[EUR][1000 genomes]
rs8036226	0.88[EUR][1000 genomes]
rs8042068	0.91[EUR][1000 genomes]
rs884584	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9302102	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs949646	0.83[ASN][1000 genomes]
rs9672572	0.82[EUR][1000 genomes]
rs9806365	0.92[ASN][1000 genomes]
rs9806647	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs999393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39913200-39924000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr15:39913400-39922400	Enhancers	Fetal Intestine Large	intestine
3	chr15:39913400-39923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:39914000-39922800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:39914200-39922600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr15:39914600-39922800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr15:39914600-39923600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr15:39914600-39923600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr15:39914600-39923800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr15:39914800-39923800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr15:39916000-39922200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr15:39916000-39924000	Enhancers	HMEC	breast
13	chr15:39916200-39922200	Enhancers	Left Ventricle	heart
14	chr15:39916200-39923400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:39916800-39921800	Enhancers	Right Ventricle	heart
17	chr15:39917400-39923800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:39917600-39926200	Weak transcription	Esophagus	oesophagus
19	chr15:39918000-39922200	Enhancers	HepG2	liver
20	chr15:39918400-39921800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:39918800-39923400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:39919400-39921800	Enhancers	Lung	lung
23	chr15:39919400-39922000	Enhancers	Fetal Muscle Leg	muscle
24	chr15:39919400-39922400	Enhancers	Duodenum Mucosa	Duodenum
25	chr15:39919400-39922600	Enhancers	Fetal Lung	lung
26	chr15:39919400-39922600	Enhancers	GM12878-XiMat	blood
27	chr15:39919400-39923000	Enhancers	Fetal Brain Male	brain
28	chr15:39919800-39922000	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr15:39920000-39921800	Enhancers	Fetal Muscle Trunk	muscle
30	chr15:39920000-39921800	Enhancers	HSMMtube	muscle
31	chr15:39920000-39922000	Enhancers	Small Intestine	intestine
32	chr15:39920000-39922200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:39920000-39922200	Enhancers	Right Atrium	heart
34	chr15:39920000-39923400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr15:39920000-39923600	Enhancers	HUVEC	blood vessel
36	chr15:39920000-39924400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:39920200-39922000	Enhancers	NHLF	lung
38	chr15:39920200-39922800	Enhancers	Fetal Thymus	thymus
39	chr15:39920200-39924400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:39920400-39922000	Enhancers	Fetal Stomach	stomach
41	chr15:39920400-39922000	Enhancers	HSMM	muscle
42	chr15:39920400-39922200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr15:39920600-39922400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr15:39920600-39924200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:39920800-39922000	Enhancers	Adipose Nuclei	Adipose
46	chr15:39920800-39922000	Weak transcription	Fetal Kidney	kidney
47	chr15:39920800-39922200	Enhancers	Colon Smooth Muscle	Colon
48	chr15:39920800-39922800	Enhancers	Primary T cells from cord blood	blood
49	chr15:39920800-39924400	Enhancers	NHEK	skin
50	chr15:39920800-39925200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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