Variant report

Variant	rs2415129
Chromosome Location	chr15:72191266-72191267
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	chr15:72180763..72183209-chr15:72189285..72191973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066933	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11072341	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072343	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1120002	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11856068	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12437582	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12438532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12439689	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12439773	0.86[EUR][1000 genomes]
rs12440299	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12441470	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441567	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441622	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12443127	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12592806	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593857	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12593946	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1471688	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1545825	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16953747	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16956539	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1805020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805021	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1871834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1905337	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979459	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277544	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291279	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306575	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415124	0.89[AFR][1000 genomes]
rs2415125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2625526	0.85[ASN][1000 genomes]
rs2723357	0.87[AFR][1000 genomes]
rs2742321	0.85[AFR][1000 genomes]
rs28639924	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28653163	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28658271	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28701834	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2899774	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2929514	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929515	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2929521	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2929522	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2929524	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2929530	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2929531	1.00[ASW][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2929533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2957369	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957726	0.87[ASN][1000 genomes]
rs2957729	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957730	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957733	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2957741	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957747	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957748	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34625473	0.80[ASN][1000 genomes]
rs35696756	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35773391	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3759812	0.81[EUR][1000 genomes]
rs3825869	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4511484	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4776583	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777472	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6494976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162134	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7164646	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7172281	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8032957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8033997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034436	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8182066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981695	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920148	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv569906	chr15:72126034-72218036	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv516871	chr15:72126034-72325595	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv904336	chr15:72145937-72329906	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv569907	chr15:72154000-72215065	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv569908	chr15:72154000-72218036	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv457195	chr15:72177659-72250741	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv569909	chr15:72177659-72250741	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72122400-72195000	Weak transcription	NHEK	skin
2	chr15:72122600-72195800	Weak transcription	Gastric	stomach
3	chr15:72131800-72192800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:72142600-72199200	Weak transcription	Hela-S3	cervix
5	chr15:72144600-72223400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:72161000-72211000	Weak transcription	Small Intestine	intestine
7	chr15:72164000-72218400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:72167000-72197800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:72170200-72194000	Weak transcription	Fetal Intestine Small	intestine
10	chr15:72171200-72192600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:72172400-72192000	Weak transcription	Thymus	Thymus
12	chr15:72173000-72200600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:72176000-72193400	Weak transcription	Psoas Muscle	Psoas
14	chr15:72177400-72192400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:72178200-72193800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:72178400-72195000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:72178800-72195000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:72182400-72193600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:72183800-72192000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:72183800-72192000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:72183800-72192200	Weak transcription	Brain Angular Gyrus	brain
22	chr15:72183800-72192400	Weak transcription	Brain Substantia Nigra	brain
23	chr15:72184200-72192400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:72185600-72191600	Weak transcription	Fetal Heart	heart
25	chr15:72185600-72198600	Weak transcription	A549	lung
26	chr15:72185800-72192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:72188800-72193200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:72189200-72192400	Strong transcription	Osteobl	bone
29	chr15:72189200-72198000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:72189400-72191400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr15:72189400-72192400	Strong transcription	Primary B cells from cord blood	blood
32	chr15:72189400-72192400	Strong transcription	Fetal Intestine Large	intestine
33	chr15:72189400-72192400	Strong transcription	Fetal Kidney	kidney
34	chr15:72189400-72192600	Strong transcription	Primary hematopoietic stem cells	blood
35	chr15:72189400-72193800	Strong transcription	Fetal Lung	lung
36	chr15:72189400-72194000	Strong transcription	Fetal Muscle Leg	muscle
37	chr15:72189400-72194000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:72189400-72194000	Strong transcription	HSMM	muscle
39	chr15:72189400-72194200	Strong transcription	Fetal Brain Female	brain
40	chr15:72189400-72194600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:72189400-72194600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:72189400-72195000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:72189400-72195200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:72189400-72195400	Weak transcription	HepG2	liver
45	chr15:72189400-72196000	Strong transcription	NHDF-Ad	bronchial
46	chr15:72189400-72196800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:72189400-72196800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr15:72189400-72197400	Strong transcription	Adipose Nuclei	Adipose
49	chr15:72189400-72197400	Strong transcription	Placenta	Placenta
50	chr15:72189400-72197600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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