Variant report

Variant	rs61730508
Chromosome Location	chr5:68629748-68629749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr5:68629609-68629793	HepG2	liver:	n/a	n/a
2	TAF1	chr5:68629563-68629889	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:68629558-68629870	Hela-S3	cervix:	n/a	n/a
4	GABPA	chr5:68629578-68629819	GM12878	blood:	n/a	n/a
5	GABPA	chr5:68629657-68629918	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:68629556-68629972	K562	blood:	n/a	n/a
7	POLR2A	chr5:68629384-68630041	GM12892	blood:	n/a	n/a
8	POLR2A	chr5:68629655-68629951	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:68629718-68629759	MCF-7	breast:	n/a	n/a
10	TAF1	chr5:68629644-68629800	GM12891	blood:	n/a	n/a
11	POLR2A	chr5:68629436-68630034	GM12892	blood:	n/a	n/a
12	TAF1	chr5:68629640-68629887	HepG2	liver:	n/a	n/a
13	GABPA	chr5:68629554-68629815	Hela-S3	cervix:	n/a	n/a
14	TCF3	chr5:68629644-68629946	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:68629535-68630059	A549	lung:	n/a	n/a
16	HEY1	chr5:68629513-68629957	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:68629659-68629819	A549	lung:	n/a	n/a
18	TAF1	chr5:68629640-68629814	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:68629647-68629796	GM12891	blood:	n/a	n/a
20	POLR2A	chr5:68629712-68629774	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr5:68629489-68629954	GM12892	blood:	n/a	n/a
22	POLR2A	chr5:68629649-68629802	ProgFib	skin:	n/a	n/a
23	POLR2A	chr5:68629651-68629996	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:68629554-68629909	GM12891	blood:	n/a	n/a
25	POLR2A	chr5:68629651-68629815	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:68629606-68629965	Gliobla	brain:	n/a	n/a
27	POLR2A	chr5:68629538-68629977	MCF-7	breast:	n/a	n/a
28	TAF1	chr5:68629566-68629920	GM12892	blood:	n/a	n/a
29	POLR2A	chr5:68629637-68629795	H1-hESC	embryonic stem cell:	n/a	n/a
30	GABPA	chr5:68629625-68629781	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr5:68629499-68629911	Hela-S3	cervix:	n/a	n/a
32	SIN3AK20	chr5:68629662-68629783	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:68629648-68629792	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr5:68629475-68629954	HepG2	liver:	n/a	n/a
35	POLR2A	chr5:68629457-68629987	GM12892	blood:	n/a	n/a
36	HEY1	chr5:68629585-68629956	K562	blood:	n/a	n/a
37	POU2F2	chr5:68629561-68629997	GM12878	blood:	n/a	n/a
38	TAF1	chr5:68629642-68629813	GM12892	blood:	n/a	n/a
39	TAF1	chr5:68629624-68629817	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr5:68629635-68629867	GM12878	blood:	n/a	n/a
41	POLR2A	chr5:68629664-68629777	HepG2	liver:	n/a	n/a
42	POLR2A	chr5:68629500-68629891	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr5:68629704-68629784	GM12878	blood:	n/a	n/a
44	GABPA	chr5:68629655-68629811	HepG2	liver:	n/a	n/a
45	HEY1	chr5:68629533-68629907	K562	blood:	n/a	n/a
46	MYC	chr5:68629695-68629856	MCF-7	breast:	n/a	n/a
47	TAF1	chr5:68629556-68629910	HepG2	liver:	n/a	n/a
48	TAF1	chr5:68629629-68629807	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:68629666-68629787	A549	lung:	n/a	n/a
50	POLR2A	chr5:68629665-68629819	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:68629714-68629764	PANC-1	pancreas:	n/a
2	chr5:68629714-68629764	HRCEpiC	kidney:	n/a
3	chr5:68629714-68629764	Caco-2	colon:	n/a
4	chr5:68629714-68629764	NHBE	bronchial:	n/a
5	chr5:68629714-68629764	Hela-S3	cervix:	n/a
6	chr5:68629714-68629764	IMR90	lung:	fetal
7	chr5:68629714-68629764	HNPCEpiC	eye:	n/a
8	chr5:68629714-68629764	HRPEpiC	eye:	n/a
9	chr5:68629714-68629764	HIPEpiC	eye:	n/a
10	chr5:68629714-68629764	SK-N-MC	brain:	n/a
11	chr5:68629714-68629764	HMEC	breast:	n/a
12	chr5:68629714-68629764	T-47D	breast:	n/a
13	chr5:68629714-68629764	NT2-D1	testis:	n/a
14	chr5:68629714-68629764	Jurkat	blood:	n/a
15	chr5:68629714-68629764	SKMC	muscle:	n/a
16	chr5:68629714-68629764	HRE	kidney:	n/a
17	chr5:68629714-68629764	SK-N-SH_RA	brain:	n/a
18	chr5:68629714-68629764	RPTEC	kidney:	n/a
19	chr5:68629714-68629764	HL-60	blood:	n/a
20	chr5:68629714-68629764	HEK293	kidney:	embryo
21	chr5:68629714-68629764	BE2_C	brain:	n/a
22	chr5:68629714-68629764	PFSK-1	brain:	n/a
23	chr5:68629714-68629764	AG09319	gingival:	n/a
24	chr5:68629714-68629764	K562	blood:	n/a
25	chr5:68629714-68629764	AG04449	skin:	fetal
26	chr5:68629714-68629764	SAEC	small airway:	n/a
27	chr5:68629714-68629764	GM12878	blood:	n/a
28	chr5:68629714-68629764	HUVEC	blood vessel:	n/a
29	chr5:68629714-68629764	NB4	blood:	n/a
30	chr5:68629714-68629764	ProgFib	skin:	n/a
31	chr5:68629714-68629764	HPAEpiC	pulmonary alveolar:	n/a
32	chr5:68629714-68629764	ovcar-3	ovarian:	n/a
33	chr5:68629714-68629764	GM12891	blood:	n/a
34	chr5:68629714-68629764	GM19239	blood:	n/a
35	chr5:68629714-68629764	MCF-7	breast:	n/a
36	chr5:68629714-68629764	HAEpiC	amniotic membrane:	n/a
37	chr5:68629714-68629764	HCPEpiC	choroid plexus:	n/a
38	chr5:68629714-68629764	AG09309	skin:	n/a
39	chr5:68629714-68629764	AG10803	skin:	n/a
40	chr5:68629714-68629764	ECC-1	luminal epithelium:	n/a
41	chr5:68629714-68629764	HepG2	liver:	n/a
42	chr5:68629714-68629764	GM06990	blood:	n/a
43	chr5:68629714-68629764	H1-hESC	embryonic stem cell:	embryo
44	chr5:68629714-68629764	SK-N-SH	brain:	n/a
45	chr5:68629714-68629764	AoSMC	blood vessel:	n/a
46	chr5:68629714-68629764	Hepatocyte	liver:	n/a
47	chr5:68629714-68629764	HCF	heart:	n/a
48	chr5:68629714-68629764	CMK	blood:	n/a
49	chr5:68629714-68629764	HCM	heart:	n/a
50	chr5:68629714-68629764	NHDF-neo	bronchial:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68628802..68630677-chr5:68662896..68664873,2	K562	blood:
2	chr5:68628027..68630302-chr5:68663373..68666765,3	K562	blood:
3	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
4	chr5:68626462..68633259-chr5:68656360..68665608,14	MCF-7	breast:
5	chr5:68513358..68515252-chr5:68629266..68631706,2	K562	blood:
6	chr5:68628511..68630857-chr5:68714273..68716319,2	MCF-7	breast:
7	chr5:68388706..68391393-chr5:68627238..68631529,6	MCF-7	breast:

No data

Variant related genes	Relation type
CHCHD2P2	TF binding region
CCDC125	TF binding region
CCDC125	CpG island
CHCHD2P2	CpG island
ENSG00000152939	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17236331	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17271888	1.00[ASN][1000 genomes]
rs62371187	1.00[ASN][1000 genomes]
rs62371222	1.00[ASN][1000 genomes]
rs62371224	1.00[ASN][1000 genomes]
rs62371695	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62373160	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv969960	chr5:68613678-68646127	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3515528	chr5:68624487-68653938	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3515529	chr5:68624487-68653938	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv968922	chr5:68628679-68631659	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68628800-68649200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:68629000-68629800	Enhancers	Primary T cells fromperipheralblood	blood
3	chr5:68629000-68629800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr5:68629000-68629800	Weak transcription	Brain Angular Gyrus	brain
5	chr5:68629000-68629800	Enhancers	HepG2	liver
6	chr5:68629000-68630000	Enhancers	Fetal Heart	heart
7	chr5:68629000-68630000	Enhancers	Pancreas	Pancrea
8	chr5:68629000-68630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:68629000-68630400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:68629000-68630400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:68629000-68630400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:68629000-68630400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:68629000-68630400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:68629000-68630400	Weak transcription	Brain Anterior Caudate	brain
15	chr5:68629000-68630400	Weak transcription	Brain Germinal Matrix	brain
16	chr5:68629000-68630400	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:68629000-68630400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:68629000-68630400	Weak transcription	Brain Substantia Nigra	brain
19	chr5:68629000-68630400	Weak transcription	NHEK	skin
20	chr5:68629000-68630600	Weak transcription	Adipose Nuclei	Adipose
21	chr5:68629000-68630600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:68629000-68630600	Weak transcription	Small Intestine	intestine
23	chr5:68629000-68630600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr5:68629000-68630600	Weak transcription	Osteobl	bone
25	chr5:68629000-68630800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:68629000-68630800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr5:68629000-68630800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:68629000-68630800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:68629000-68630800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:68629000-68630800	Weak transcription	K562	blood
31	chr5:68629000-68631000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:68629000-68631000	Weak transcription	Fetal Intestine Small	intestine
33	chr5:68629000-68631000	Enhancers	Fetal Muscle Trunk	muscle
34	chr5:68629000-68631200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:68629000-68631200	Weak transcription	HMEC	breast
36	chr5:68629000-68631800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:68629000-68645800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:68629000-68646000	Weak transcription	Primary T cells from cord blood	blood
39	chr5:68629000-68646800	Weak transcription	NH-A	brain
40	chr5:68629200-68629800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:68629200-68630400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:68629200-68630400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr5:68629200-68630400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:68629200-68630400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:68629200-68630400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr5:68629200-68630400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:68629200-68630400	Weak transcription	Hela-S3	cervix
48	chr5:68629200-68630600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:68629200-68630600	Weak transcription	Primary B cells from cord blood	blood
50	chr5:68629200-68630600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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