Variant report

Variant	rs61546369
Chromosome Location	chr15:52304429-52304430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52303163..52304907-chr15:52331339..52333174,2	MCF-7	breast:
2	chr15:52262466..52265779-chr15:52303817..52307426,4	MCF-7	breast:
3	chr15:52300735..52303050-chr15:52304162..52305762,3	MCF-7	breast:
4	chr15:52295795..52300731-chr15:52301222..52304726,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10152141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518675	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16964694	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964700	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964705	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16964720	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17540338	0.81[ASN][1000 genomes]
rs17612255	0.88[ASN][1000 genomes]
rs17612326	0.81[ASN][1000 genomes]
rs2001741	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017967	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2246726	0.91[ASN][1000 genomes]
rs2306793	0.86[EUR][1000 genomes]
rs2414120	0.88[ASN][1000 genomes]
rs2414123	0.93[ASN][1000 genomes]
rs2441779	0.91[ASN][1000 genomes]
rs2470593	0.91[ASN][1000 genomes]
rs2470594	0.91[ASN][1000 genomes]
rs2470595	0.93[ASN][1000 genomes]
rs2554340	0.88[ASN][1000 genomes]
rs2899484	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099571	0.88[ASN][1000 genomes]
rs4375608	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4456445	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4774606	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775993	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4775995	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775996	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55705935	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55714716	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs55873482	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307802	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56677715	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58000475	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs58936667	0.83[ASN][1000 genomes]
rs7177328	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359204	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74013636	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013638	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013640	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013642	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013644	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013645	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013646	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013647	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013648	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013653	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs74013654	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74013656	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013657	0.88[ASN][1000 genomes]
rs74013659	0.81[ASN][1000 genomes]
rs74013661	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7497554	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751560	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8033365	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033840	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8036048	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8040728	0.82[ASN][1000 genomes]
rs8041281	0.91[ASN][1000 genomes]
rs9796534	0.91[AMR][1000 genomes];0.98[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	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv517399	chr15:52266878-52305464	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1536	chr15:52276293-52320919	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52299400-52310800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:52299600-52305400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:52299600-52305600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:52299600-52310200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:52299600-52310600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:52299600-52310800	Weak transcription	HSMMtube	muscle
7	chr15:52301200-52305400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:52301200-52305600	Weak transcription	Primary T cells from cord blood	blood
9	chr15:52301400-52310800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:52301400-52310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:52301400-52310800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:52301400-52310800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:52301600-52304600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr15:52301600-52305400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:52301600-52305600	Enhancers	GM12878-XiMat	blood
16	chr15:52301600-52306000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:52301800-52304800	Enhancers	HepG2	liver
18	chr15:52301800-52306200	Weak transcription	Primary B cells from cord blood	blood
19	chr15:52302400-52306000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:52302800-52306400	Enhancers	HMEC	breast
21	chr15:52303000-52304600	Enhancers	Rectal Smooth Muscle	rectum
22	chr15:52303000-52304800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:52303000-52304800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr15:52303000-52304800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:52303000-52304800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:52303000-52305800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:52303200-52304600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:52303200-52304600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:52303200-52304600	Enhancers	Colon Smooth Muscle	Colon
30	chr15:52303200-52304600	Enhancers	NHDF-Ad	bronchial
31	chr15:52303200-52304800	Enhancers	Brain Angular Gyrus	brain
32	chr15:52303400-52304600	Enhancers	Brain Germinal Matrix	brain
33	chr15:52303400-52304800	Enhancers	Adipose Nuclei	Adipose
34	chr15:52303400-52304800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:52303400-52304800	Enhancers	Brain Substantia Nigra	brain
36	chr15:52303600-52304800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr15:52303600-52305400	Weak transcription	HSMM	muscle
38	chr15:52303600-52306200	Enhancers	A549	lung
39	chr15:52303600-52310800	Weak transcription	Pancreas	Pancrea
40	chr15:52303600-52310800	Weak transcription	Right Atrium	heart
41	chr15:52303800-52304600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:52303800-52305200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:52303800-52305800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:52303800-52306000	Enhancers	HUVEC	blood vessel
45	chr15:52303800-52306200	Enhancers	NHEK	skin
46	chr15:52303800-52306800	Enhancers	K562	blood
47	chr15:52303800-52310400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:52303800-52310600	Weak transcription	Osteobl	bone
49	chr15:52304000-52304600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:52304000-52304600	Flanking Active TSS	Brain Hippocampus Middle	brain

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