Variant report

Variant	rs4910440
Chromosome Location	chr11:9114999-9115000
allele	C/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	CTCF	chr11:9114860-9115010	HAc	cerebellar:	n/a	chr11:9114890-9114903
2	RAD21	chr11:9114670-9115102	A549	lung:	n/a	n/a
3	CTCF	chr11:9114720-9115071	GM12878	blood:	n/a	chr11:9114890-9114903
4	CTCF	chr11:9114860-9115010	HRE	kidney:	n/a	chr11:9114890-9114903
5	CTCF	chr11:9114860-9115010	HMEC	breast:	n/a	chr11:9114890-9114903
6	CTCF	chr11:9114860-9115010	HFF-Myc	foreskin:	n/a	chr11:9114890-9114903
7	CTCF	chr11:9114668-9115178	MCF-7	breast:	n/a	chr11:9114890-9114903
8	CTCF	chr11:9114536-9115295	A549	lung:	n/a	chr11:9114890-9114903
9	RAD21	chr11:9114771-9115030	HepG2	liver:	n/a	n/a
10	RAD21	chr11:9114788-9115010	SK-N-SH_RA	brain:	n/a	n/a
11	MAX	chr11:9114797-9115146	MCF-7	breast:	n/a	chr11:9114928-9114939
12	CTCF	chr11:9114860-9115010	RPTEC	kidney:	n/a	chr11:9114890-9114903
13	CTCF	chr11:9114860-9115010	HVMF	connective:	n/a	chr11:9114890-9114903
14	CTCF	chr11:9114880-9115030	NHEK	skin:	n/a	chr11:9114890-9114903
15	CTCF	chr11:9114860-9115010	GM06990	blood:	n/a	chr11:9114890-9114903
16	CTCF	chr11:9114860-9115010	Hela-S3	cervix:	n/a	chr11:9114890-9114903
17	RAD21	chr11:9114620-9115047	MCF-7	breast:	n/a	n/a
18	ARID3A	chr11:9114802-9115029	HepG2	liver:	n/a	n/a
19	RAD21	chr11:9114715-9115124	HCT-116	colon:	n/a	n/a
20	CTCF	chr11:9114900-9115050	AG04450	lung:	n/a	n/a
21	SMC3	chr11:9114738-9115006	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr11:9114775-9115004	Hela-S3	cervix:	n/a	chr11:9114890-9114903
23	CTCF	chr11:9114860-9115010	HCT-116	colon:	n/a	chr11:9114890-9114903
24	CTCF	chr11:9114738-9115050	IMR90	lung:	n/a	chr11:9114890-9114903
25	CTCF	chr11:9114960-9115110	A549	lung:	n/a	n/a
26	RAD21	chr11:9114631-9115110	MCF-7	breast:	n/a	n/a
27	CTCF	chr11:9114571-9115174	HCT-116	colon:	n/a	chr11:9114890-9114903
28	CTCF	chr11:9114900-9115050	HEEpiC	esophagus:	n/a	n/a
29	RAD21	chr11:9114737-9115057	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr11:9114759-9115055	MCF-7	breast:	n/a	chr11:9114890-9114903
31	CTCF	chr11:9114761-9115032	K562	blood:	n/a	chr11:9114890-9114903
32	CTCF	chr11:9114880-9115030	GM12865	blood:	n/a	chr11:9114890-9114903
33	MYC	chr11:9114964-9115026	MCF10A-Er-Src	breast:	n/a	n/a
34	CTCF	chr11:9114365-9115326	SK-N-SH	brain:	n/a	chr11:9114890-9114903
35	RAD21	chr11:9114586-9115167	SK-N-SH	brain:	n/a	n/a
36	CTCF	chr11:9114860-9115010	HCPEpiC	choroid plexus:	n/a	chr11:9114890-9114903
37	RAD21	chr11:9114780-9115015	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9114505..9115469-chr11:9158990..9159883,2	MCF-7	breast:
2	chr11:9108004..9116385-chr11:9156452..9162678,21	MCF-7	breast:
3	chr11:9114649..9115533-chr11:9142208..9142895,3	MCF-7	breast:
4	chr11:9113356..9115182-chr11:9141033..9143763,3	MCF-7	breast:
5	chr11:9109700..9116224-chr11:9155740..9163743,14	MCF-7	breast:
6	chr11:9114626..9115314-chr11:9154013..9154891,3	MCF-7	breast:

Variant related genes	Relation type
MIR5691	TF binding region
SCUBE2	TF binding region
KRT8P41	TF binding region
ENSG00000175356	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7105754	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv467704	chr11:9059192-9125301	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv553454	chr11:9059192-9125301	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv467706	chr11:9077652-9114999	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv553455	chr11:9077652-9114999	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4910440	ILK	cis	cerebellum	SCAN
rs4910440	OR56A1	cis	cerebellum	SCAN
rs4910440	SCUBE2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9116200	Enhancers	Pancreas	Pancrea
2	chr11:9113600-9118600	Weak transcription	Right Atrium	heart
3	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
4	chr11:9113800-9115000	Weak transcription	Adipose Nuclei	Adipose
5	chr11:9113800-9115200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:9113800-9115400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr11:9114000-9115400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:9114200-9122000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:9114200-9136200	Weak transcription	Fetal Heart	heart
10	chr11:9114400-9115000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:9114400-9115000	Enhancers	HSMM	muscle
12	chr11:9114800-9115000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
13	chr11:9114800-9117000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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