Variant report

Variant	rs334611
Chromosome Location	chr2:179167766-179167767
allele	C/T
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: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10182749	0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs10497513	0.86[CHB][hapmap]
rs10497514	0.86[CHB][hapmap]
rs10930829	0.86[CHB][hapmap]
rs12471986	0.84[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs12479027	0.81[CHB][hapmap]
rs12618595	0.81[CHB][hapmap]
rs13386703	0.85[ASN][1000 genomes]
rs13400415	0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs13402976	0.89[MEX][hapmap]
rs13404410	0.87[ASN][1000 genomes]
rs1368905	0.91[CHB][hapmap]
rs1434089	0.86[CHB][hapmap]
rs16866226	0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs16866231	0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs16866247	0.88[ASN][1000 genomes]
rs16866270	0.85[JPT][hapmap]
rs1812550	0.86[CHB][hapmap]
rs333988	0.85[EUR][1000 genomes]
rs334602	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334603	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334606	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334608	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813253	0.81[CHB][hapmap]
rs4894005	0.82[EUR][1000 genomes]
rs4894013	0.89[MEX][hapmap]
rs55682490	0.88[ASN][1000 genomes]
rs55707762	0.88[ASN][1000 genomes]
rs55992481	0.88[ASN][1000 genomes]
rs56002997	0.88[ASN][1000 genomes]
rs58505502	0.88[ASN][1000 genomes]
rs62176069	0.80[EUR][1000 genomes]
rs62176070	0.80[EUR][1000 genomes]
rs62179160	0.82[EUR][1000 genomes]
rs62179161	0.82[EUR][1000 genomes]
rs62179165	0.82[EUR][1000 genomes]
rs6433718	0.84[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6433722	0.86[CHB][hapmap]
rs6743122	0.82[EUR][1000 genomes]
rs6754517	0.86[CHB][hapmap]
rs6760059	0.88[MEX][hapmap]
rs6761421	0.86[CHB][hapmap]
rs7349264	0.80[EUR][1000 genomes]
rs7576995	0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs964165	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs334611	ATP5G3	cis	parietal	SCAN
rs334611	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:21 , 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	chr2:179163800-179174200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:179164000-179173400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:179164200-179169400	Weak transcription	NHEK	skin
10	chr2:179164200-179180400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:179164600-179173800	Weak transcription	HMEC	breast
12	chr2:179164600-179200800	Weak transcription	Aorta	Aorta
13	chr2:179164800-179168800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:179164800-179168800	Weak transcription	K562	blood
15	chr2:179165200-179173600	Weak transcription	Esophagus	oesophagus
16	chr2:179165200-179177800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:179165400-179174800	Weak transcription	Gastric	stomach
18	chr2:179166800-179170800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:179166800-179179400	Weak transcription	Psoas Muscle	Psoas
20	chr2:179167000-179179400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:179167000-179179400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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