Variant report

Variant	rs13400415
Chromosome Location	chr2:179165803-179165804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179057856..179060542-chr2:179163868..179166036,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs101266	1.00[YRI][hapmap]
rs10182749	1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151447	0.90[CHB][hapmap]
rs12464536	0.90[EUR][1000 genomes]
rs12471790	0.82[CHB][hapmap]
rs12474802	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12474844	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12476671	1.00[YRI][hapmap]
rs12618660	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs12620577	0.82[EUR][1000 genomes]
rs12620729	0.82[EUR][1000 genomes]
rs13386703	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13404410	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13406155	0.88[AFR][1000 genomes]
rs1434083	0.82[CHB][hapmap]
rs1434086	0.90[EUR][1000 genomes]
rs147180	1.00[YRI][hapmap]
rs16866202	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16866226	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16866231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866247	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866256	0.90[EUR][1000 genomes]
rs16866270	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs16866271	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16866273	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs16866275	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs16866281	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[EUR][1000 genomes]
rs16866299	1.00[CEU][hapmap]
rs1982104	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs28676734	0.88[AFR][1000 genomes]
rs333997	1.00[YRI][hapmap]
rs334009	1.00[YRI][hapmap]
rs334013	1.00[YRI][hapmap]
rs334014	1.00[YRI][hapmap]
rs334602	0.83[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs334603	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs334606	0.89[ASN][1000 genomes]
rs334608	0.89[ASN][1000 genomes]
rs334611	0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs334613	0.83[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs3813252	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs551368	1.00[YRI][hapmap]
rs55682490	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55707762	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719869	1.00[EUR][1000 genomes]
rs55992481	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56002997	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56148541	0.90[EUR][1000 genomes]
rs58505502	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708349	1.00[AFR][1000 genomes]
rs718650	0.90[EUR][1000 genomes]
rs718651	0.90[EUR][1000 genomes]
rs7562824	0.88[AFR][1000 genomes]
rs7567412	0.98[AFR][1000 genomes]
rs7576995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989738	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179143200-179188600	Weak transcription	Brain Anterior Caudate	brain
2	chr2:179155600-179174200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:179160200-179188600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:179161600-179173600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:179162000-179174200	Weak transcription	Adipose Nuclei	Adipose
6	chr2:179162400-179179800	Weak transcription	Liver	Liver
7	chr2:179162800-179166600	Enhancers	HUVEC	blood vessel
8	chr2:179163800-179174200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:179164000-179166200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:179164000-179173400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:179164200-179166200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:179164200-179169400	Weak transcription	NHEK	skin
13	chr2:179164200-179180400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:179164600-179173800	Weak transcription	HMEC	breast
15	chr2:179164600-179200800	Weak transcription	Aorta	Aorta
16	chr2:179164800-179168800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:179164800-179168800	Weak transcription	K562	blood
18	chr2:179165200-179173600	Weak transcription	Esophagus	oesophagus
19	chr2:179165200-179177800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:179165400-179166400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:179165400-179174800	Weak transcription	Gastric	stomach
22	chr2:179165600-179166400	Weak transcription	Psoas Muscle	Psoas
23	chr2:179165600-179166800	Weak transcription	Hela-S3	cervix

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