Variant report

Variant	rs16969487
Chromosome Location	chr15:39935022-39935023
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	chr15:39934745..39936337-chr15:39938200..39940638,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10083552	1.00[JPT][hapmap]
rs10152903	1.00[CHB][hapmap]
rs10152951	1.00[CHB][hapmap]
rs1038097	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1051442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10520141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10520145	1.00[JPT][hapmap]
rs10520146	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10520152	1.00[JPT][hapmap]
rs1073675	1.00[CHB][hapmap]
rs12324682	1.00[JPT][hapmap]
rs1382443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1382444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16969167	1.00[CHB][hapmap]
rs16969335	1.00[JPT][hapmap]
rs16969338	1.00[JPT][hapmap]
rs16969352	1.00[JPT][hapmap]
rs16969491	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16969547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16969663	1.00[CHB][hapmap]
rs16969664	1.00[CHB][hapmap]
rs16969666	1.00[CHB][hapmap]
rs16969672	1.00[CHB][hapmap]
rs16969679	1.00[CHB][hapmap]
rs16969680	1.00[CHB][hapmap]
rs16969688	1.00[CHB][hapmap]
rs17632916	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17633107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17633210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17705806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17706083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17706179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17717859	1.00[CHB][hapmap]
rs1813493	0.91[EUR][1000 genomes]
rs1988082	0.82[EUR][1000 genomes]
rs1988555	0.85[EUR][1000 genomes]
rs1994380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2129457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2228262	1.00[CHB][hapmap]
rs2228263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2411316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618156	0.91[EUR][1000 genomes]
rs2618160	0.91[EUR][1000 genomes]
rs2618161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2618164	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2618165	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2618167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2664123	0.91[EUR][1000 genomes]
rs2664136	0.91[EUR][1000 genomes]
rs2664137	0.91[EUR][1000 genomes]
rs2664138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs2664140	0.91[EUR][1000 genomes]
rs2664142	0.91[EUR][1000 genomes]
rs28377784	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28549326	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28619289	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28653011	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878675	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4085744	0.82[AMR][1000 genomes]
rs41315060	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4415979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4503768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45461294	0.95[EUR][1000 genomes]
rs4923835	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs58188999	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59578395	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59628570	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6492905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs7172155	1.00[CHB][hapmap]
rs7173948	1.00[CHB][hapmap]
rs7179604	1.00[CHB][hapmap]
rs7181354	1.00[CHB][hapmap]
rs7182423	1.00[CHB][hapmap]
rs74008647	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74008648	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8036035	1.00[JPT][hapmap]
rs8041266	1.00[CHB][hapmap]
rs880270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937961	1.00[CHB][hapmap]
rs937962	1.00[CHB][hapmap]
rs954152	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9972350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:39921400-39937600	Weak transcription	Psoas Muscle	Psoas
3	chr15:39923800-39939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:39931400-39935600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:39931400-39937000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:39932200-39935400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:39932600-39935400	Enhancers	HMEC	breast
8	chr15:39932600-39935400	Enhancers	HUVEC	blood vessel
9	chr15:39932800-39935200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:39933000-39935200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:39933000-39935400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr15:39933000-39936000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr15:39933200-39935400	Enhancers	Colon Smooth Muscle	Colon
14	chr15:39933400-39935200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:39933400-39935400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:39933600-39935200	Enhancers	NH-A	brain
17	chr15:39933600-39935400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:39933800-39935200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:39933800-39935200	Enhancers	Rectal Smooth Muscle	rectum
20	chr15:39933800-39935400	Enhancers	NHDF-Ad	bronchial
21	chr15:39933800-39935400	Enhancers	Osteobl	bone
22	chr15:39933800-39937000	Weak transcription	HepG2	liver
23	chr15:39933800-39937800	Enhancers	HSMM	muscle
24	chr15:39934000-39935200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:39934000-39936400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:39934000-39937400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:39934200-39935400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:39934200-39938000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:39934400-39935400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr15:39934400-39936000	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr15:39934600-39935200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:39934600-39935200	Enhancers	Hela-S3	cervix
33	chr15:39934800-39935200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr15:39934800-39935400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:39934800-39936000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:39934800-39936200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:39934800-39936400	Weak transcription	Left Ventricle	heart
38	chr15:39934800-39936400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:39934800-39936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:39934800-39937400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr15:39934800-39937600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr15:39934800-39937600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:39934800-39937600	Weak transcription	Esophagus	oesophagus
44	chr15:39934800-39937600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:39934800-39937800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr15:39934800-39937800	Enhancers	NHEK	skin
47	chr15:39934800-39938200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:39935000-39936400	Weak transcription	HSMMtube	muscle
49	chr15:39935000-39936800	Weak transcription	Fetal Heart	heart

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