Variant report

Variant	rs6416501
Chromosome Location	chr15:73370302-73370303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73366653..73368204-chr15:73368418..73370771,2	MCF-7	breast:
2	chr15:73356525..73360663-chr15:73369090..73372368,3	MCF-7	breast:
3	chr15:73343238..73345497-chr15:73369477..73372153,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10467949	0.94[ASN][1000 genomes]
rs11632639	0.98[ASN][1000 genomes]
rs11856922	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899246	0.94[ASN][1000 genomes]
rs12916928	0.99[ASN][1000 genomes]
rs1479337	0.94[ASN][1000 genomes]
rs2010793	0.94[ASN][1000 genomes]
rs28481558	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28743094	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28842482	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35060813	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4132535	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4777582	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4777583	0.98[ASN][1000 genomes]
rs4777589	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4777591	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6416502	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495047	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164894	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172021	0.81[ASN][1000 genomes]
rs7172396	0.81[ASN][1000 genomes]
rs7173142	0.98[ASN][1000 genomes]
rs7175329	0.94[ASN][1000 genomes]
rs7495458	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026579	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs922516	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9920186	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73359200-73370600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr15:73361000-73372400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:73365000-73374000	Enhancers	Brain Angular Gyrus	brain
4	chr15:73365800-73370600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:73366000-73370800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:73366800-73370600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:73367000-73371800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:73367200-73370800	Weak transcription	Fetal Lung	lung
9	chr15:73367800-73370800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:73368000-73370600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:73368000-73370800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:73368000-73370800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:73368000-73370800	Weak transcription	Fetal Intestine Small	intestine
14	chr15:73368000-73371000	Weak transcription	Fetal Intestine Large	intestine
15	chr15:73368200-73370800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:73368200-73370800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:73368200-73370800	Weak transcription	NHEK	skin
18	chr15:73368200-73375600	Enhancers	Brain Substantia Nigra	brain
19	chr15:73368200-73381000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:73368400-73370800	Weak transcription	Hela-S3	cervix
21	chr15:73368400-73371000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:73368400-73373200	Enhancers	Brain Anterior Caudate	brain
23	chr15:73368600-73370800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:73368600-73371000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:73368600-73375200	Weak transcription	Aorta	Aorta
26	chr15:73368800-73370400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:73368800-73371800	Enhancers	Rectal Smooth Muscle	rectum
28	chr15:73369000-73370600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:73369200-73374600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:73369600-73374200	Enhancers	Brain Hippocampus Middle	brain
31	chr15:73369600-73374400	Enhancers	Brain Cingulate Gyrus	brain
32	chr15:73369800-73370600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr15:73370000-73371600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr15:73370000-73371800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr15:73370000-73372200	Enhancers	Duodenum Mucosa	Duodenum
36	chr15:73370000-73373800	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr15:73370200-73370400	Enhancers	Esophagus	oesophagus
38	chr15:73370200-73370400	Enhancers	Fetal Brain Male	brain
39	chr15:73370200-73370400	Enhancers	Gastric	stomach
40	chr15:73370200-73370600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:73370200-73370600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:73370200-73371000	Enhancers	Ovary	ovary
43	chr15:73370200-73371200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:73370200-73371200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:73370200-73371200	Enhancers	Pancreas	Pancrea
46	chr15:73370200-73371200	Enhancers	Psoas Muscle	Psoas
47	chr15:73370200-73371600	Enhancers	Small Intestine	intestine
48	chr15:73370200-73371800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:73370200-73371800	Enhancers	Colon Smooth Muscle	Colon
50	chr15:73370200-73372000	Enhancers	Rectal Mucosa Donor 29	rectum

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