Variant report

Variant	rs2129457
Chromosome Location	chr15:39983621-39983622
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39974204..39976528-chr15:39982397..39984405,2	MCF-7	breast:
2	chr15:39980861..39985158-chr15:39988045..39992700,5	K562	blood:

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

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10083552	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10152903	1.00[CHB][hapmap]
rs10152951	1.00[CHB][hapmap]
rs1051442	1.00[CHB][hapmap]
rs10520141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10520143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10520145	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10520146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520149	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs10520150	0.83[AFR][1000 genomes]
rs10520152	1.00[JPT][hapmap]
rs1073675	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs12324669	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs12324682	1.00[JPT][hapmap]
rs1382443	1.00[CHB][hapmap]
rs1382444	1.00[CHB][hapmap]
rs16969167	1.00[CHB][hapmap]
rs16969335	1.00[JPT][hapmap]
rs16969338	1.00[JPT][hapmap]
rs16969352	1.00[JPT][hapmap]
rs16969484	0.86[ASN][1000 genomes]
rs16969487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs16969491	1.00[CHB][hapmap]
rs16969547	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969573	0.86[ASN][1000 genomes]
rs16969662	0.81[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs16969663	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs16969664	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs16969666	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs16969672	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap]
rs16969678	0.86[ASN][1000 genomes]
rs16969679	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs16969680	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs16969688	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs16969692	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs16969701	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs16969702	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs16969718	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs16969723	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs16969724	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs17633107	1.00[CHB][hapmap]
rs17633210	1.00[CHB][hapmap]
rs17705806	1.00[CHB][hapmap]
rs17706083	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17706179	1.00[CHB][hapmap]
rs17717859	1.00[CHB][hapmap]
rs1994380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129455	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs2171309	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs2228262	1.00[CHB][hapmap]
rs2228263	1.00[CHB][hapmap]
rs2411316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2618161	1.00[CHB][hapmap]
rs2618165	1.00[JPT][hapmap]
rs2618167	1.00[CHB][hapmap]
rs2664138	1.00[CHB][hapmap]
rs28377784	0.80[EUR][1000 genomes]
rs28417668	0.81[AFR][1000 genomes]
rs28421798	0.81[AFR][1000 genomes]
rs28421809	0.85[AFR][1000 genomes]
rs28457210	0.83[AFR][1000 genomes]
rs28514641	0.83[AFR][1000 genomes]
rs28519658	0.80[AFR][1000 genomes]
rs28549326	0.80[EUR][1000 genomes]
rs28568868	0.83[AFR][1000 genomes]
rs28570392	0.82[AFR][1000 genomes]
rs28585060	0.83[AFR][1000 genomes]
rs28619289	0.80[EUR][1000 genomes]
rs28625134	0.92[AFR][1000 genomes]
rs28626090	0.85[AFR][1000 genomes]
rs28629181	0.83[AFR][1000 genomes]
rs28653011	0.80[EUR][1000 genomes]
rs28657849	0.83[AFR][1000 genomes]
rs28735552	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28785006	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34878675	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4085744	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4322636	0.86[ASN][1000 genomes]
rs4415979	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4503768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923835	1.00[CHB][hapmap]
rs4923838	0.81[CEU][hapmap]
rs55674415	0.85[AFR][1000 genomes]
rs55899942	0.88[AFR][1000 genomes]
rs56862147	0.90[AFR][1000 genomes]
rs56916119	0.83[AFR][1000 genomes]
rs58878379	0.90[AFR][1000 genomes]
rs59146042	0.86[ASN][1000 genomes]
rs59628570	0.85[EUR][1000 genomes]
rs60228643	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6492905	1.00[CHB][hapmap]
rs7171057	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs7172138	0.84[AFR][1000 genomes]
rs7172155	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs7172346	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs7173948	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs7179604	1.00[CHB][hapmap]
rs7180740	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs7181354	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7181875	0.85[AFR][1000 genomes]
rs7182423	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7183462	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs72727029	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72727047	0.87[AFR][1000 genomes]
rs72727060	0.88[AFR][1000 genomes]
rs72727067	0.81[AFR][1000 genomes]
rs72727068	0.83[AFR][1000 genomes]
rs72727070	0.82[AFR][1000 genomes]
rs74008648	0.80[EUR][1000 genomes]
rs74008680	0.85[AFR][1000 genomes]
rs8036035	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8041266	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs880270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs937961	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs937962	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs9972350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39974800-39985000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:39975400-39984400	Weak transcription	Fetal Kidney	kidney
3	chr15:39977200-39990600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:39979800-39985000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:39982000-39985800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr15:39982400-39983800	Enhancers	K562	blood
7	chr15:39982600-39985800	Enhancers	Fetal Stomach	stomach
8	chr15:39982800-39983800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:39982800-39985000	Enhancers	Fetal Lung	lung
10	chr15:39982800-39985200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:39982800-39986200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:39982800-39986400	Enhancers	Brain Germinal Matrix	brain
13	chr15:39983000-39984800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:39983000-39985800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:39983000-39989800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:39983200-39983800	Enhancers	NHDF-Ad	bronchial
17	chr15:39983200-39984000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr15:39983200-39984000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:39983200-39984200	Weak transcription	Brain Anterior Caudate	brain
20	chr15:39983200-39985000	Enhancers	Fetal Brain Female	brain
21	chr15:39983200-39985000	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:39983200-39985400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:39983200-39985800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr15:39983200-39990800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:39983400-39985800	Enhancers	Fetal Brain Male	brain
26	chr15:39983600-39983800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:39983600-39984800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:39983600-39986200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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