Variant report

Variant	rs2952523
Chromosome Location	chr7:25606113-25606114
allele	A/T
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	SMC3	chr7:25604902-25607116	SK-N-SH	brain:	n/a	chr7:25605656-25605670 chr7:25605700-25605714
2	CTCF	chr7:25605201-25606159	HepG2	liver:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
3	CTCF	chr7:25605218-25606150	HCT-116	colon:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
4	CTCF	chr7:25605087-25606278	HCT-116	colon:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
5	CTCF	chr7:25606040-25606190	HA-sp	spinal cord:	n/a	n/a
6	RAD21	chr7:25603664-25607366	SK-N-SH	brain:	n/a	chr7:25605652-25605671 chr7:25605661-25605670 chr7:25605696-25605715
7	CTCF	chr7:25604949-25606365	A549	lung:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716
8	GATA3	chr7:25605620-25606148	SH-SY5Y	brain:	n/a	chr7:25605691-25605701
9	CTCF	chr7:25606060-25606210	GM12867	blood:	n/a	n/a
10	CTCF	chr7:25606040-25606190	BE2_C	brain:	n/a	n/a
11	CTCF	chr7:25604546-25607266	SK-N-SH	brain:	n/a	chr7:25605699-25605715 chr7:25605661-25605668 chr7:25605693-25605714 chr7:25605654-25605672 chr7:25605700-25605713 chr7:25605649-25605670 chr7:25605655-25605671 chr7:25605698-25605716

No.	Distal block	Cell Line	Cell type
1	chr7:25433474..25434141-chr7:25605268..25606353,4	K562	blood:
2	chr7:25298973..25299854-chr7:25605283..25606167,4	MCF-7	breast:
3	chr7:25429055..25432240-chr7:25604579..25606349,45	MCF-7	breast:
4	chr7:25605406..25606179-chr7:25890948..25891905,5	K562	blood:
5	chr7:25430622..25431559-chr7:25605393..25606130,7	MCF-7	breast:
6	chr7:25428848..25430407-chr7:25605173..25606452,6	MCF-7	breast:
7	chr7:25433157..25433791-chr7:25605378..25606157,2	MCF-7	breast:
8	chr7:25298951..25300126-chr7:25605192..25606795,18	K562	blood:
9	chr7:25298470..25299852-chr7:25605228..25606576,11	MCF-7	breast:
10	chr7:25605147..25606187-chr7:25890189..25892015,14	MCF-7	breast:
11	chr7:25605629..25606130-chr7:26404535..26405453,2	K562	blood:
12	chr7:25430463..25431643-chr7:25605112..25606187,14	K562	blood:

Variant related genes	Relation type
ENSG00000222101	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10486406	0.93[ASN][1000 genomes]
rs10951078	0.93[ASN][1000 genomes]
rs11973587	0.82[ASN][1000 genomes]
rs11973605	0.88[ASN][1000 genomes]
rs11973620	0.82[ASN][1000 genomes]
rs12667261	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12669889	0.89[ASN][1000 genomes]
rs12670768	0.93[ASN][1000 genomes]
rs1354264	0.93[ASN][1000 genomes]
rs1553398	0.83[ASN][1000 genomes]
rs1553399	0.93[ASN][1000 genomes]
rs16873895	0.93[ASN][1000 genomes]
rs16873899	0.93[ASN][1000 genomes]
rs16873909	0.88[ASN][1000 genomes]
rs17151904	0.82[ASN][1000 genomes]
rs1818146	0.93[ASN][1000 genomes]
rs28473276	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2960821	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs60277994	0.80[ASN][1000 genomes]
rs62454590	0.90[ASN][1000 genomes]
rs62454591	0.93[ASN][1000 genomes]
rs62454592	0.93[ASN][1000 genomes]
rs739622	0.93[ASN][1000 genomes]
rs975369	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
4	nsv522815	chr7:25599858-25606120	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv523322	chr7:25601480-25606120	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv525378	chr7:25605725-25615221	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25604000-25606200	Enhancers	Fetal Lung	lung
2	chr7:25604600-25608200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:25604800-25608200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:25605200-25606400	Weak transcription	Fetal Stomach	stomach
5	chr7:25605200-25606800	Enhancers	Fetal Kidney	kidney
6	chr7:25605400-25607000	Enhancers	Stomach Mucosa	stomach
7	chr7:25605600-25606800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:25606000-25606400	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:25606000-25607400	Weak transcription	Rectal Mucosa Donor 31	rectum

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