Variant report

Variant	rs7002551
Chromosome Location	chr8:9178135-9178136
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	RAD21	chr8:9178117-9178458	HepG2	liver:	n/a	chr8:9178273-9178282 chr8:9178269-9178288 chr8:9178274-9178286
2	CTCF	chr8:9177938-9179010	A549	lung:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
3	RAD21	chr8:9178028-9178479	A549	lung:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
4	CTCF	chr8:9178092-9178464	GM12878	blood:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
5	RAD21	chr8:9178010-9178519	H1-hESC	embryonic stem cell:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
6	RAD21	chr8:9178042-9178550	ECC-1	luminal epithelium:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
7	CTCF	chr8:9178085-9178502	H1-hESC	embryonic stem cell:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
8	RAD21	chr8:9178105-9178473	H1-hESC	embryonic stem cell:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
9	ZNF143	chr8:9178100-9178477	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr8:9178114-9178424	A549	lung:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
11	ZNF143	chr8:9178109-9178441	GM12878	blood:	n/a	n/a
12	RAD21	chr8:9178127-9178453	Hela-S3	cervix:	n/a	chr8:9178273-9178282 chr8:9178269-9178288 chr8:9178274-9178286
13	RAD21	chr8:9178015-9178596	HCT-116	colon:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
14	CTCF	chr8:9178100-9178250	AG04450	lung:	n/a	n/a
15	NFE2	chr8:9178117-9178158	GM12878	blood:	n/a	n/a
16	RAD21	chr8:9178017-9178536	A549	lung:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
17	CTCF	chr8:9178054-9178640	SK-N-SH	brain:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
18	RAD21	chr8:9178052-9178467	SK-N-SH_RA	brain:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
19	CTCF	chr8:9178100-9178250	HMEC	breast:	n/a	n/a
20	CTCF	chr8:9178100-9178452	K562	blood:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
21	CTCF	chr8:9178075-9178394	A549	lung:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
22	CTCF	chr8:9178120-9178270	NHDF-neo	bronchial:	n/a	n/a
23	RAD21	chr8:9178007-9178473	H1-hESC	embryonic stem cell:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
24	CTCF	chr8:9178067-9178468	MCF-7	breast:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
25	RAD21	chr8:9178023-9178536	ECC-1	luminal epithelium:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
26	RAD21	chr8:9177867-9178623	SK-N-SH	brain:	n/a	chr8:9178273-9178282 chr8:9178109-9178118 chr8:9178269-9178288 chr8:9178274-9178286
27	CTCF	chr8:9177998-9178422	HCT-116	colon:	n/a	chr8:9178270-9178291 chr8:9178273-9178281
28	CTCF	chr8:9178019-9178460	MCF-7	breast:	n/a	chr8:9178270-9178291 chr8:9178273-9178281

No.	Distal block	Cell Line	Cell type
1	chr8:9177828..9179105-chr8:9195409..9196219,4	MCF-7	breast:
2	chr8:9177871..9178799-chr8:9195168..9196018,3	MCF-7	breast:
3	chr8:9178042..9178608-chr8:9688275..9689205,2	MCF-7	breast:
4	chr8:9177588..9178247-chr8:9534308..9535009,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254235	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10099512	1.00[CHB][hapmap]
rs10106829	0.86[ASN][1000 genomes]
rs11778774	0.86[ASN][1000 genomes]
rs11779870	1.00[CHB][hapmap]
rs11781511	0.86[ASN][1000 genomes]
rs11990096	1.00[CHB][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs12543276	0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13264007	0.86[ASN][1000 genomes]
rs13265179	0.86[ASN][1000 genomes]
rs13274716	0.86[ASN][1000 genomes]
rs13279173	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1461729	0.86[ASN][1000 genomes]
rs17660635	1.00[ASN][1000 genomes]
rs17661330	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17716118	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2054345	0.86[ASN][1000 genomes]
rs2126259	0.86[ASN][1000 genomes]
rs2126260	0.86[ASN][1000 genomes]
rs2126261	1.00[CHB][hapmap]
rs2126263	0.86[ASN][1000 genomes]
rs2126264	0.86[ASN][1000 genomes]
rs2169385	0.86[ASN][1000 genomes]
rs2169387	0.86[ASN][1000 genomes]
rs28529330	1.00[ASN][1000 genomes]
rs330090	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs330091	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330092	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs330093	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs330095	0.87[ASN][1000 genomes]
rs330096	0.87[ASN][1000 genomes]
rs34025891	0.86[ASN][1000 genomes]
rs34271262	0.86[ASN][1000 genomes]
rs34906420	0.86[ASN][1000 genomes]
rs35899262	0.86[ASN][1000 genomes]
rs4240624	0.86[ASN][1000 genomes]
rs4332138	0.86[ASN][1000 genomes]
rs4841132	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4841133	0.86[ASN][1000 genomes]
rs60191553	0.86[ASN][1000 genomes]
rs6601299	0.86[ASN][1000 genomes]
rs6984305	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6985493	0.86[ASN][1000 genomes]
rs6998846	1.00[ASN][1000 genomes]
rs7004769	0.86[ASN][1000 genomes]
rs73535309	0.86[ASN][1000 genomes]
rs7357361	1.00[CHB][hapmap]
rs7464067	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9772631	1.00[ASN][1000 genomes]
rs983308	1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983309	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs983310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983311	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987289	1.00[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1018847	chr8:9017110-9216354	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1022967	chr8:9023771-9261351	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv539462	chr8:9023771-9261351	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7002551	DEFA5	cis	parietal	SCAN
rs7002551	LARGE	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9174600-9178400	Enhancers	Brain Cingulate Gyrus	brain
2	chr8:9174600-9178800	Enhancers	Brain Substantia Nigra	brain
3	chr8:9174800-9178600	Enhancers	Brain Hippocampus Middle	brain
4	chr8:9175200-9178600	Enhancers	Brain Anterior Caudate	brain
5	chr8:9175400-9182400	Enhancers	Liver	Liver
6	chr8:9175800-9178600	Enhancers	Left Ventricle	heart
7	chr8:9175800-9179000	Enhancers	Fetal Heart	heart
8	chr8:9176200-9178400	Enhancers	Fetal Intestine Large	intestine
9	chr8:9176400-9178200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr8:9176400-9181600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr8:9176600-9181000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr8:9176800-9179200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr8:9177000-9182000	Weak transcription	Right Ventricle	heart
14	chr8:9177200-9178200	Weak transcription	Right Atrium	heart
15	chr8:9177200-9182600	Weak transcription	Psoas Muscle	Psoas
16	chr8:9177400-9178600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:9177800-9178400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:9178000-9182000	Weak transcription	Adipose Nuclei	Adipose

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