Variant report

Variant	rs6561647
Chromosome Location	chr13:52340750-52340751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52156494..52159056-chr13:52340175..52342392,2	MCF-7	breast:
2	chr13:52022483..52024400-chr13:52339695..52341730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139668	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs617452	1.00[AMR][1000 genomes]
rs6561642	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74086279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52308200-52342800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr13:52322600-52342200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:52322600-52342200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr13:52323000-52343400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr13:52323200-52341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr13:52324800-52342600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr13:52326000-52342600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr13:52327600-52343200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:52327800-52343000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:52330400-52341800	Weak transcription	Hela-S3	cervix
11	chr13:52330600-52355600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:52332600-52342800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr13:52333000-52342600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:52333000-52343600	Weak transcription	Psoas Muscle	Psoas
15	chr13:52333200-52342400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:52334400-52343800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:52335000-52343200	Weak transcription	Ovary	ovary
18	chr13:52335200-52347000	Weak transcription	Fetal Brain Male	brain
19	chr13:52335200-52348000	Weak transcription	Fetal Brain Female	brain
20	chr13:52336400-52342400	Weak transcription	Fetal Heart	heart
21	chr13:52336600-52342200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:52336600-52342400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr13:52336800-52341600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr13:52336800-52342400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:52337400-52340800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr13:52337800-52342200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr13:52338600-52341000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr13:52338600-52342600	Strong transcription	NHEK	skin
29	chr13:52338800-52342400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:52338800-52343000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr13:52339200-52341400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr13:52339200-52341600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr13:52339200-52342600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:52339400-52342400	Weak transcription	Left Ventricle	heart
35	chr13:52339400-52342400	Weak transcription	Right Atrium	heart
36	chr13:52339400-52342400	Weak transcription	Right Ventricle	heart
37	chr13:52339400-52342400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr13:52339400-52342800	Strong transcription	Primary B cells from cord blood	blood
39	chr13:52339400-52343400	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr13:52339400-52343800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr13:52339400-52343800	Weak transcription	Brain Anterior Caudate	brain
42	chr13:52339400-52343800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:52339400-52345000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr13:52339400-52347000	Weak transcription	A549	lung
45	chr13:52339400-52347600	Weak transcription	Aorta	Aorta
46	chr13:52339400-52347600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:52339400-52347800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr13:52339400-52349600	Weak transcription	Placenta	Placenta
49	chr13:52339400-52352000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr13:52339400-52356200	Weak transcription	Rectal Mucosa Donor 31	rectum

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