Variant report

Variant	rs16972887
Chromosome Location	chr15:42522558-42522559
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	chr15:42518203..42520282-chr15:42521732..42524296,3	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10220859	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs12437600	0.92[ASN][1000 genomes]
rs12438240	0.86[CHB][hapmap]
rs12438369	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs12438453	0.86[CHB][hapmap]
rs12438509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441016	0.94[ASN][1000 genomes]
rs12441642	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1624183	1.00[CEU][hapmap]
rs1659213	1.00[CEU][hapmap]
rs1659218	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs1659219	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs1659221	0.81[AMR][1000 genomes]
rs1659222	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs1678984	0.81[AMR][1000 genomes]
rs1678992	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs16972770	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16972776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs16972779	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16973060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1703754	1.00[CEU][hapmap]
rs2138831	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2407707	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2412688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2412709	0.85[CHB][hapmap]
rs2620386	1.00[CEU][hapmap]
rs28364388	0.84[ASN][1000 genomes]
rs28364393	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2918460	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs3736099	0.89[ASN][1000 genomes]
rs3743005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3743007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3743008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3825785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4506867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4923932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924631	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4924644	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924674	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs55882551	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56257215	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56670003	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56702977	0.84[ASN][1000 genomes]
rs56987883	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57134130	0.84[ASN][1000 genomes]
rs57393446	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57933952	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57973092	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57976413	1.00[ASN][1000 genomes]
rs58292736	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58313689	0.92[ASN][1000 genomes]
rs58712370	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59094161	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59132828	0.95[ASN][1000 genomes]
rs59138723	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59320762	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59893734	0.89[ASN][1000 genomes]
rs59974698	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60443443	0.89[ASN][1000 genomes]
rs60634548	1.00[ASN][1000 genomes]
rs61069354	1.00[ASN][1000 genomes]
rs61133768	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6493033	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678778	1.00[CEU][hapmap]
rs681029	1.00[CEU][hapmap]
rs7179203	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7179709	1.00[CEU][hapmap]
rs7180279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7181979	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73398938	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400993	0.89[ASN][1000 genomes]
rs73402707	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73403365	1.00[ASN][1000 genomes]
rs73403548	0.81[AMR][1000 genomes]
rs73407403	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73407407	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73407488	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409577	0.97[ASN][1000 genomes]
rs74009020	0.81[AMR][1000 genomes]
rs8025601	0.86[CHB][hapmap];0.95[ASN][1000 genomes]
rs8027016	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041951	0.88[AMR][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	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS 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	12 gene(s)	inside rSNPs	diseases
6	nsv1054102	chr15:42493052-42528765	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
2	chr15:42501000-42534800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:42501000-42536600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:42501000-42536800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:42501000-42538000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:42501200-42523200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:42501200-42532400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr15:42501800-42536800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:42502000-42535000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:42502200-42534000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:42502200-42536600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:42502800-42535200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:42502800-42536400	Strong transcription	Fetal Muscle Leg	muscle
14	chr15:42503200-42544000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:42506800-42532000	Strong transcription	Placenta	Placenta
16	chr15:42508000-42532200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:42508200-42525000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:42509400-42535200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:42511800-42536800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:42513200-42523600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:42513200-42532200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:42513800-42534800	Strong transcription	Liver	Liver
23	chr15:42514000-42523600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:42514000-42526600	Strong transcription	Left Ventricle	heart
25	chr15:42514000-42534800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:42514000-42535200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:42514200-42522600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:42514200-42523400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr15:42514200-42524200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr15:42514200-42526600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:42514200-42527000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:42514200-42532400	Strong transcription	Adipose Nuclei	Adipose
33	chr15:42514200-42535200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:42514200-42535200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:42514400-42531800	Strong transcription	Primary T cells from cord blood	blood
36	chr15:42514400-42533600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr15:42514400-42534800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:42514400-42535000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:42514400-42535000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:42514400-42536400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr15:42514400-42536400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:42514400-42537200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:42514600-42523800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:42514600-42523800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:42514600-42535000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:42514800-42532000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:42515000-42535400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr15:42515000-42544600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr15:42515200-42523200	Strong transcription	Osteobl	bone
50	chr15:42515200-42526400	Strong transcription	Primary hematopoietic stem cells	blood

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