Variant report

Variant	rs2068599
Chromosome Location	chr13:53424055-53424056
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:122)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr13:53423976-53425385	H1-hESC	embryonic stem cell:	n/a	chr13:53425004-53425014 chr13:53425128-53425138 chr13:53424048-53424058
2	CTBP2	chr13:53423916-53425961	H1-hESC	embryonic stem cell:	n/a	n/a
3	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
4	POLR2A	chr13:53423515-53426172	H1-neurons	neurons:	n/a	n/a
5	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
6	MAX	chr13:53423778-53424120	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUND	chr13:53423496-53425372	H1-hESC	embryonic stem cell:	n/a	chr13:53424314-53424328
8	SP1	chr13:53423776-53425122	H1-hESC	embryonic stem cell:	n/a	chr13:53424503-53424516
9	E2F6	chr13:53423616-53424175	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr13:53423939-53424150	H1-hESC	embryonic stem cell:	n/a	n/a
11	MXI1	chr13:53423946-53425593	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:53424049-53424099	HUVEC	blood vessel:	n/a
2	chr13:53424049-53424099	AG04449	skin:	fetal
3	chr13:53424049-53424099	NHDF-neo	bronchial:	n/a
4	chr13:53424032-53424082	HCT-116	colon:	n/a
5	chr13:53424049-53424099	HMEC	breast:	n/a
6	chr13:53424032-53424082	HRPEpiC	eye:	n/a
7	chr13:53424049-53424099	SK-N-MC	brain:	n/a
8	chr13:53424032-53424082	Jurkat	blood:	n/a
9	chr13:53424049-53424099	HAEpiC	amniotic membrane:	n/a
10	chr13:53424032-53424082	Caco-2	colon:	n/a
11	chr13:53424049-53424099	SKMC	muscle:	n/a
12	chr13:53424049-53424099	HRPEpiC	eye:	n/a
13	chr13:53424032-53424082	HEEpiC	esophagus:	n/a
14	chr13:53424032-53424082	ProgFib	skin:	n/a
15	chr13:53424032-53424082	ECC-1	luminal epithelium:	n/a
16	chr13:53424049-53424099	BE2_C	brain:	n/a
17	chr13:53424049-53424099	BJ	skin:	n/a
18	chr13:53424049-53424099	A549	lung:	n/a
19	chr13:53424032-53424082	MCF-7	breast:	n/a
20	chr13:53424049-53424099	HEK293	kidney:	embryo
21	chr13:53424049-53424099	ProgFib	skin:	n/a
22	chr13:53424032-53424082	HAEpiC	amniotic membrane:	n/a
23	chr13:53424049-53424099	PANC-1	pancreas:	n/a
24	chr13:53424032-53424082	GM12892	blood:	n/a
25	chr13:53424032-53424082	SAEC	small airway:	n/a
26	chr13:53424032-53424082	IMR90	lung:	fetal
27	chr13:53424032-53424082	HCPEpiC	choroid plexus:	n/a
28	chr13:53424032-53424082	ovcar-3	ovarian:	n/a
29	chr13:53424049-53424099	GM06990	blood:	n/a
30	chr13:53424032-53424082	SK-N-SH	brain:	n/a
31	chr13:53424032-53424082	NHBE	bronchial:	n/a
32	chr13:53424049-53424099	HCT-116	colon:	n/a
33	chr13:53424032-53424082	LNCaP	prostate:	n/a
34	chr13:53424032-53424082	GM12891	blood:	n/a
35	chr13:53424032-53424082	SK-N-SH_RA	brain:	n/a
36	chr13:53424032-53424082	Hepatocyte	liver:	n/a
37	chr13:53424032-53424082	AG09319	gingival:	n/a
38	chr13:53424049-53424099	HIPEpiC	eye:	n/a
39	chr13:53424032-53424082	CMK	blood:	n/a
40	chr13:53424049-53424099	ovcar-3	ovarian:	n/a
41	chr13:53424032-53424082	HEK293	kidney:	embryo
42	chr13:53424049-53424099	HCM	heart:	n/a
43	chr13:53424032-53424082	MCF10A-Er-Src	breast:	n/a
44	chr13:53424032-53424082	NT2-D1	testis:	n/a
45	chr13:53424032-53424082	GM12878	blood:	n/a
46	chr13:53424049-53424099	HRE	kidney:	n/a
47	chr13:53424049-53424099	U87	brain:	n/a
48	chr13:53424049-53424099	H1-hESC	embryonic stem cell:	embryo
49	chr13:53424032-53424082	HPAEpiC	pulmonary alveolar:	n/a
50	chr13:53424032-53424082	HIPEpiC	eye:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:53423777..53426647-chr13:53440227..53445526,5	MCF-7	breast:
2	chr13:53416128..53422445-chr13:53423052..53427915,11	MCF-7	breast:
3	chr13:53422829..53424558-chr13:53771804..53774307,2	MCF-7	breast:
4	chr13:53225548..53228779-chr13:53423444..53428429,4	MCF-7	breast:
5	chr13:53423819..53426475-chr13:53542000..53544855,3	MCF-7	breast:
6	chr13:53423269..53426675-chr13:53427472..53433524,8	MCF-7	breast:
7	chr13:53413901..53415786-chr13:53423425..53426036,2	MCF-7	breast:
8	chr13:53189284..53191816-chr13:53423878..53426423,2	MCF-7	breast:
9	chr13:53419410..53422161-chr13:53423908..53427048,5	MCF-7	breast:

No data

Variant related genes	Relation type
PCDH8	TF binding region
PCDH8	CpG island
ENSG00000139675	Chromatin interaction
ENSG00000250299	Chromatin interaction
ENSG00000165416	Chromatin interaction
ENSG00000225510	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs55805702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59653444	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60002541	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61618614	0.93[AMR][1000 genomes]
rs7333178	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73494250	0.93[AMR][1000 genomes]
rs73494262	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73494266	0.93[AMR][1000 genomes]
rs7987466	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8002092	0.93[AMR][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:46 , 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	chr13:53421200-53424800	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr13:53421400-53424400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
4	chr13:53421600-53424400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
5	chr13:53421800-53426200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
6	chr13:53422200-53424600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr13:53422400-53424400	Bivalent Enhancer	Fetal Thymus	thymus
8	chr13:53422600-53424400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr13:53422600-53424600	Weak transcription	Gastric	stomach
10	chr13:53422600-53424800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr13:53422600-53424800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:53422800-53424400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr13:53422800-53424600	Weak transcription	Pancreas	Pancrea
14	chr13:53422800-53424600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
15	chr13:53423000-53424600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:53423000-53424600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
17	chr13:53423000-53424600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr13:53423000-53424600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
19	chr13:53423000-53425000	Flanking Active TSS	Fetal Brain Female	brain
20	chr13:53423200-53424200	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr13:53423200-53424600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:53423200-53424600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
23	chr13:53423200-53424800	Bivalent Enhancer	Fetal Stomach	stomach
24	chr13:53423400-53424200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr13:53423400-53424200	Active TSS	Brain Anterior Caudate	brain
26	chr13:53423400-53424200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
27	chr13:53423400-53424600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:53423400-53424800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr13:53423600-53424200	Bivalent Enhancer	Right Ventricle	heart
30	chr13:53423600-53426000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
31	chr13:53423800-53424200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr13:53423800-53424200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
33	chr13:53423800-53424400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr13:53423800-53424400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
35	chr13:53423800-53424600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr13:53423800-53424600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr13:53423800-53424600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
38	chr13:53423800-53425000	ZNF genes & repeats	Spleen	Spleen
39	chr13:53423800-53426000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
40	chr13:53423800-53426800	Enhancers	Fetal Brain Male	brain
41	chr13:53424000-53424200	Weak transcription	GM12878-XiMat	blood
42	chr13:53424000-53424600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr13:53424000-53424600	Bivalent Enhancer	Pancreatic Islets	Pancreatic Islet
44	chr13:53424000-53424800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
45	chr13:53424000-53424800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
46	chr13:53424000-53424800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain

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