Variant report

Variant	rs13400738
Chromosome Location	chr2:179166160-179166161
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	chr2:179165931..179168129-chr2:179315067..179316871,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180228	Chromatin interaction
ENSG00000204311	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10203141	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10203420	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11680778	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11692144	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12469658	0.82[EUR][1000 genomes]
rs12473780	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693158	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12693160	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024959	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13382421	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13407992	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1368906	0.83[EUR][1000 genomes]
rs1434080	0.82[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1865325	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55799649	0.83[EUR][1000 genomes]
rs6716156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756651	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7587549	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9288016	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9288017	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs993598	0.81[JPT][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13400738	ATF2	cis	parietal	SCAN
rs13400738	NEUROD1	cis	cerebellum	SCAN
rs13400738	LOC100130691	cis	cerebellum	SCAN

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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