Variant report

Variant	rs73494253
Chromosome Location	chr13:53423686-53423687
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr13:53423625-53426612	H1-hESC	embryonic stem cell:	n/a	chr13:53424048-53424057 chr13:53425722-53425731 chr13:53424040-53424053 chr13:53424469-53424478 chr13:53424988-53424997 chr13:53425401-53425414
2	POLR2A	chr13:53423515-53426172	H1-neurons	neurons:	n/a	n/a
3	REST	chr13:53422663-53426246	HL-60	blood:	n/a	chr13:53424040-53424053 chr13:53422864-53422877 chr13:53424988-53425001 chr13:53425721-53425731 chr13:53424411-53424421 chr13:53425716-53425729 chr13:53422984-53422998 chr13:53422986-53422996 chr13:53425719-53425733 chr13:53424936-53424945 chr13:53424047-53424057
4	POLR2A	chr13:53423522-53423982	H1-neurons	neurons:	n/a	n/a
5	JUND	chr13:53423496-53425372	H1-hESC	embryonic stem cell:	n/a	chr13:53424314-53424328
6	E2F6	chr13:53423616-53424175	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:53416128..53422445-chr13:53423052..53427915,11	MCF-7	breast:
2	chr13:53422829..53424558-chr13:53771804..53774307,2	MCF-7	breast:
3	chr13:53225548..53228779-chr13:53423444..53428429,4	MCF-7	breast:
4	chr13:53423269..53426675-chr13:53427472..53433524,8	MCF-7	breast:
5	chr13:53413901..53415786-chr13:53423425..53426036,2	MCF-7	breast:

Variant related genes	Relation type
PCDH8	TF binding region
ENSG00000225510	Chromatin interaction
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11840632	1.00[AMR][1000 genomes]
rs11842169	1.00[AMR][1000 genomes]
rs564456	1.00[AMR][1000 genomes]
rs57622965	1.00[AMR][1000 genomes]
rs58221735	1.00[AMR][1000 genomes]
rs59233409	1.00[AMR][1000 genomes]
rs73494246	1.00[AMR][1000 genomes]
rs73494254	1.00[AMR][1000 genomes]
rs73494260	1.00[AMR][1000 genomes]
rs73494285	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73494292	1.00[AMR][1000 genomes]
rs73494295	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73496392	0.88[AFR][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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900089	chr13:53385334-53429453	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1810064	chr13:53412849-53441018	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1822518	chr13:53412849-53441018	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv1829072	chr13:53412849-53441018	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv523092	chr13:53419139-53429453	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53419600-53424400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr13:53420000-53424000	ZNF genes & repeats	GM12878-XiMat	blood
3	chr13:53421200-53424800	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr13:53421400-53424400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
5	chr13:53421600-53424400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
6	chr13:53421800-53426200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
7	chr13:53422200-53424600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr13:53422400-53424400	Bivalent Enhancer	Fetal Thymus	thymus
9	chr13:53422600-53424400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:53422600-53424600	Weak transcription	Gastric	stomach
11	chr13:53422600-53424800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr13:53422600-53424800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:53422800-53424400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr13:53422800-53424600	Weak transcription	Pancreas	Pancrea
15	chr13:53422800-53424600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
16	chr13:53423000-53423800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
17	chr13:53423000-53423800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
18	chr13:53423000-53423800	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
19	chr13:53423000-53423800	Flanking Active TSS	Fetal Brain Male	brain
20	chr13:53423000-53424000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
21	chr13:53423000-53424600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:53423000-53424600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
23	chr13:53423000-53424600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr13:53423000-53424600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr13:53423000-53425000	Flanking Active TSS	Fetal Brain Female	brain
26	chr13:53423200-53423800	Flanking Bivalent TSS/Enh	Pancreatic Islets	Pancreatic Islet
27	chr13:53423200-53423800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
28	chr13:53423200-53424200	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr13:53423200-53424600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:53423200-53424600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
31	chr13:53423200-53424800	Bivalent Enhancer	Fetal Stomach	stomach
32	chr13:53423400-53423800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
33	chr13:53423400-53424000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
34	chr13:53423400-53424200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr13:53423400-53424200	Active TSS	Brain Anterior Caudate	brain
36	chr13:53423400-53424200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
37	chr13:53423400-53424600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr13:53423400-53424800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr13:53423600-53423800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr13:53423600-53423800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr13:53423600-53423800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:53423600-53424200	Bivalent Enhancer	Right Ventricle	heart
43	chr13:53423600-53426000	Bivalent/Poised TSS	Primary T cells from cord blood	blood

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