Variant report

Variant	rs1724617
Chromosome Location	chr15:52759316-52759317
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	chr15:52754471..52760057-chr15:52770956..52773396,5	MCF-7	breast:
2	chr15:52758367..52760443-chr15:52760570..52762927,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10444827	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11637651	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11638118	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12593858	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1534201	0.96[EUR][1000 genomes]
rs1615028	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs1626180	1.00[YRI][hapmap]
rs1632403	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1669859	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1669865	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1669868	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669871	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1669875	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1669876	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1693500	1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1693511	1.00[YRI][hapmap]
rs1693513	0.91[ASN][1000 genomes]
rs1693520	0.98[ASN][1000 genomes]
rs1693521	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1724584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1724586	1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs1724613	1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs1724614	0.98[ASN][1000 genomes]
rs1724615	0.98[ASN][1000 genomes]
rs1724640	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1967624	0.80[EUR][1000 genomes]
rs2444012	0.86[EUR][1000 genomes]
rs2444014	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2444017	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2444018	0.80[ASN][1000 genomes]
rs2453983	0.98[ASN][1000 genomes]
rs2462855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2693459	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2693463	0.98[ASN][1000 genomes]
rs4238392	0.93[ASN][1000 genomes]
rs59277991	1.00[AFR][1000 genomes]
rs62015997	0.86[AFR][1000 genomes]
rs62016004	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62016006	0.80[EUR][1000 genomes]
rs7178682	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52753600-52762600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:52755600-52759400	Enhancers	Primary B cells from cord blood	blood
3	chr15:52755800-52759400	Enhancers	Primary B cells from peripheral blood	blood
4	chr15:52756200-52759400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:52756800-52759400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:52757200-52770400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:52757400-52759400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr15:52757400-52759400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:52757400-52761200	Weak transcription	NHLF	lung
10	chr15:52757400-52771800	Weak transcription	Primary T cells from cord blood	blood
11	chr15:52758000-52759400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr15:52758000-52759400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr15:52758200-52759400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr15:52758200-52759400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr15:52758200-52761000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:52758400-52759400	Enhancers	Brain Angular Gyrus	brain
17	chr15:52758400-52759800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr15:52758600-52772000	Weak transcription	HUVEC	blood vessel
19	chr15:52758600-52773000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:52758800-52760200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr15:52758800-52773000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:52759000-52759400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr15:52759000-52762200	Weak transcription	Psoas Muscle	Psoas
24	chr15:52759000-52772000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:52759200-52759800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr15:52759200-52760000	Enhancers	GM12878-XiMat	blood
27	chr15:52759200-52760200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:52759200-52761600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:52759200-52761800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:52759200-52762200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:52759200-52763800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:52759200-52770600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:52759200-52771000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:52759200-52778200	Weak transcription	Right Atrium	heart

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