Variant report

Variant	rs1253027
Chromosome Location	chr10:99491948-99491949
allele	A/G
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	RAD21	chr10:99491327-99491991	H1-hESC	embryonic stem cell:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
2	RAD21	chr10:99491173-99492123	SK-N-SH	brain:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
3	CTCF	chr10:99491424-99491961	MCF-7	breast:	n/a	chr10:99491695-99491713 chr10:99491690-99491711 chr10:99491697-99491710
4	CTCF	chr10:99491281-99492030	HCT-116	colon:	n/a	chr10:99491695-99491713 chr10:99491690-99491711 chr10:99491697-99491710
5	RAD21	chr10:99491376-99492023	ECC-1	luminal epithelium:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
6	RAD21	chr10:99491337-99491963	IMR90	lung:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
7	RAD21	chr10:99491249-99492059	HCT-116	colon:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
8	RAD21	chr10:99491407-99491962	A549	lung:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
9	SMC3	chr10:99491328-99492012	HepG2	liver:	n/a	chr10:99491697-99491711
10	CTCF	chr10:99491012-99492465	A549	lung:	n/a	chr10:99491695-99491713 chr10:99491690-99491711 chr10:99491697-99491710
11	SMC3	chr10:99491203-99491965	Hela-S3	cervix:	n/a	chr10:99491697-99491711
12	SMC3	chr10:99491089-99492179	SK-N-SH	brain:	n/a	chr10:99491697-99491711
13	RAD21	chr10:99491300-99492084	MCF-7	breast:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
14	CTCF	chr10:99491456-99491949	K562	blood:	n/a	chr10:99491695-99491713 chr10:99491690-99491711 chr10:99491697-99491710
15	RAD21	chr10:99491470-99491989	GM12878	blood:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
16	RAD21	chr10:99491368-99491991	HepG2	liver:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
17	TEAD4	chr10:99491445-99492003	ECC-1	luminal epithelium:	n/a	n/a
18	CTCF	chr10:99491237-99492111	HCT-116	colon:	n/a	chr10:99491695-99491713 chr10:99491690-99491711 chr10:99491697-99491710
19	RAD21	chr10:99491220-99491993	ECC-1	luminal epithelium:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
20	CTCF	chr10:99491427-99491987	MCF-7	breast:	n/a	chr10:99491695-99491713 chr10:99491690-99491711 chr10:99491697-99491710
21	RAD21	chr10:99491168-99492096	HCT-116	colon:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
22	RAD21	chr10:99491293-99492001	A549	lung:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
23	RAD21	chr10:99491443-99491986	MCF-7	breast:	n/a	chr10:99491696-99491709 chr10:99491693-99491712
24	CTCF	chr10:99491121-99492231	SK-N-SH	brain:	n/a	chr10:99491695-99491713 chr10:99491690-99491711 chr10:99491697-99491710
25	CTCF	chr10:99491514-99491999	K562	blood:	n/a	chr10:99491695-99491713 chr10:99491690-99491711 chr10:99491697-99491710

No.	Distal block	Cell Line	Cell type
1	chr10:99460906..99461905-chr10:99491204..99492125,3	K562	blood:
2	chr10:99460859..99461872-chr10:99491251..99492160,9	MCF-7	breast:
3	chr10:99435936..99437099-chr10:99490664..99492104,9	K562	blood:
4	chr10:99467434..99470349-chr10:99491482..99494563,3	MCF-7	breast:
5	chr10:99473776..99476718-chr10:99490535..99492237,2	K562	blood:
6	chr10:99436228..99437666-chr10:99491411..99492160,6	MCF-7	breast:
7	chr10:99468809..99469891-chr10:99491266..99492143,11	MCF-7	breast:
8	chr10:99332125..99332702-chr10:99491238..99492185,4	K562	blood:
9	chr10:99466947..99470987-chr10:99489059..99494674,5	MCF-7	breast:
10	chr10:99488183..99489718-chr10:99490230..99493190,2	MCF-7	breast:
11	chr10:99438113..99439939-chr10:99491888..99494551,2	K562	blood:
12	chr10:99471949..99474880-chr10:99491345..99493268,2	MCF-7	breast:
13	chr10:99469170..99469682-chr10:99491300..99492162,2	MCF-7	breast:

Variant related genes	Relation type
ZFYVE27	TF binding region
ENSG00000165887	Chromatin interaction
ENSG00000155254	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10786370	0.84[CHD][hapmap];0.83[MEX][hapmap]
rs1253024	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1253025	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253026	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981237	0.81[CHD][hapmap]
rs3814560	0.81[CHD][hapmap]
rs4244329	0.81[CHD][hapmap]
rs4593946	0.84[MEX][hapmap]
rs4917784	0.80[MEX][hapmap]
rs4919135	0.85[CEU][hapmap]
rs4919136	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4919137	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894678	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7907679	0.84[CHD][hapmap]
rs946780	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1253027	DHDPSL	cis	cerebellum	SCAN
rs1253027	ZFYVE27	cis	cerebellum	SCAN
rs1253027	ZFYVE27	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99478800-99496400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:99486800-99496000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:99486800-99496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:99486800-99496400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:99486800-99496400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:99486800-99496400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:99486800-99496400	Weak transcription	Pancreas	Pancrea
8	chr10:99486800-99496600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:99487000-99496000	Weak transcription	K562	blood
10	chr10:99487000-99496400	Weak transcription	Brain Anterior Caudate	brain
11	chr10:99487000-99496400	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:99487000-99496400	Weak transcription	A549	lung
13	chr10:99487200-99496400	Weak transcription	NHEK	skin
14	chr10:99487200-99496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:99487600-99496000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:99489200-99496200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr10:99491200-99492000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:99491200-99492000	Enhancers	Hela-S3	cervix
19	chr10:99491400-99492000	Enhancers	HSMM	muscle
20	chr10:99491400-99492000	Enhancers	Osteobl	bone
21	chr10:99491600-99492000	Enhancers	HMEC	breast
22	chr10:99491600-99492000	Enhancers	HSMMtube	muscle
23	chr10:99491600-99496400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:99491600-99496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:99491600-99496400	Weak transcription	Brain Substantia Nigra	brain
26	chr10:99491600-99496400	Weak transcription	NHDF-Ad	bronchial
27	chr10:99491600-99496400	Weak transcription	NHLF	lung
28	chr10:99491800-99492200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr10:99491800-99495400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:99491800-99496200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr10:99491800-99496400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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