Variant report

Variant	rs12440927
Chromosome Location	chr15:72595888-72595889
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	chr15:72594284..72596932-chr15:72765825..72768164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261423	Chromatin interaction
ENSG00000166233	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11072354	1.00[EUR][1000 genomes]
rs11072355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072356	0.83[ASN][1000 genomes]
rs11072357	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11072359	0.82[EUR][1000 genomes]
rs11629508	0.87[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11635828	0.83[ASN][1000 genomes]
rs11636289	0.83[ASN][1000 genomes]
rs11637797	0.83[ASN][1000 genomes]
rs12438836	0.87[EUR][1000 genomes]
rs12439580	0.87[EUR][1000 genomes]
rs12440204	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs12440435	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12441246	1.00[CEU][hapmap]
rs12443329	0.87[EUR][1000 genomes]
rs12591975	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12592785	1.00[EUR][1000 genomes]
rs12593082	1.00[CEU][hapmap]
rs12911449	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12914971	0.91[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs1426168	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs16953770	1.00[CEU][hapmap]
rs16956599	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs16956602	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs16956723	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2162235	0.83[ASN][1000 genomes]
rs2278150	0.82[JPT][hapmap]
rs2288256	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2288258	0.86[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2305705	1.00[CEU][hapmap]
rs28576571	0.87[EUR][1000 genomes]
rs28694144	0.87[EUR][1000 genomes]
rs2912205	0.98[ASN][1000 genomes]
rs2912226	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2912228	0.82[YRI][hapmap]
rs2912229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2959913	0.82[AFR][1000 genomes]
rs2959915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959938	0.83[ASN][1000 genomes]
rs3087652	0.82[CHD][hapmap];0.90[GIH][hapmap];0.83[ASN][1000 genomes]
rs34625473	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs35949555	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803388	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs4442765	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4606667	0.83[ASN][1000 genomes]
rs4776591	0.83[ASN][1000 genomes]
rs55792138	0.81[ASN][1000 genomes]
rs61481811	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495000	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs67849115	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7161909	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7165735	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs7167257	0.87[EUR][1000 genomes]
rs7171446	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs7175907	1.00[CEU][hapmap]
rs7178613	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs73438485	0.97[ASN][1000 genomes]
rs73438486	0.99[ASN][1000 genomes]
rs73438487	0.96[ASN][1000 genomes]
rs8025332	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8026600	0.82[ASN][1000 genomes]
rs8026894	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs8029218	1.00[CEU][hapmap]
rs8031264	0.88[AFR][1000 genomes]
rs8032276	0.82[YRI][hapmap]
rs8043345	0.87[EUR][1000 genomes]
rs8192363	0.87[EUR][1000 genomes]
rs8192381	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs9972606	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72566000-72611400	Weak transcription	Right Ventricle	heart
2	chr15:72567000-72611800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:72573200-72603000	Weak transcription	Fetal Intestine Large	intestine
4	chr15:72573800-72596200	Weak transcription	Liver	Liver
5	chr15:72573800-72597200	Weak transcription	Brain Anterior Caudate	brain
6	chr15:72578000-72611800	Weak transcription	Ovary	ovary
7	chr15:72579000-72598200	Weak transcription	Brain Germinal Matrix	brain
8	chr15:72579600-72602400	Weak transcription	Primary T cells from cord blood	blood
9	chr15:72580800-72598200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:72581200-72598600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:72582000-72608000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:72582000-72611800	Weak transcription	Spleen	Spleen
13	chr15:72582600-72598600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:72583800-72611600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:72585600-72598200	Weak transcription	Fetal Stomach	stomach
16	chr15:72590200-72604800	Weak transcription	Aorta	Aorta
17	chr15:72590600-72607600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:72590800-72602000	Weak transcription	Left Ventricle	heart
19	chr15:72592600-72597600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:72594400-72596800	Weak transcription	Primary B cells from cord blood	blood
21	chr15:72595000-72596000	Strong transcription	Adipose Nuclei	Adipose
22	chr15:72595000-72596400	Strong transcription	Brain Hippocampus Middle	brain
23	chr15:72595200-72596200	Weak transcription	Fetal Intestine Small	intestine
24	chr15:72595400-72604600	Weak transcription	Lung	lung
25	chr15:72595600-72597400	Weak transcription	Brain Substantia Nigra	brain
26	chr15:72595600-72598000	Weak transcription	Brain Angular Gyrus	brain
27	chr15:72595600-72598400	Weak transcription	Brain Inferior Temporal Lobe	brain

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