Variant report

Variant	rs245178
Chromosome Location	chr5:127203192-127203193
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	chr5:127203116..127205040-chr5:127209595..127211869,3	MCF-7	breast:
2	chr5:127163372..127165051-chr5:127202469..127205145,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs122730	0.96[CEU][hapmap]
rs1421750	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs151849	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs151855	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs151879	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151880	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151881	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151882	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151883	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs151884	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs151885	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1579284	0.80[ASN][1000 genomes]
rs181746	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245156	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs245158	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs245167	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs245177	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245180	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245182	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245183	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245186	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245187	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245191	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245192	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245193	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245194	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245195	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245197	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs245198	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs245199	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs245200	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs245201	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs245221	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs245237	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs245310	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs245311	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs245313	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs245314	0.92[EUR][1000 genomes]
rs245327	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2764766	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6864687	0.82[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs245178	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127188400-127203600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:127192600-127203200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:127194200-127213800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:127198200-127206600	Weak transcription	NHEK	skin
5	chr5:127198400-127211600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:127199400-127206600	Weak transcription	Aorta	Aorta
7	chr5:127200600-127206600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:127202000-127203600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:127202400-127203400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:127202400-127203400	Enhancers	Fetal Intestine Small	intestine
11	chr5:127202600-127203800	Enhancers	Fetal Intestine Large	intestine
12	chr5:127202600-127204000	Enhancers	Duodenum Mucosa	Duodenum
13	chr5:127202800-127203200	Enhancers	Fetal Kidney	kidney
14	chr5:127202800-127203400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:127202800-127203400	Enhancers	Stomach Mucosa	stomach
16	chr5:127202800-127204000	Enhancers	Hela-S3	cervix
17	chr5:127203000-127203200	Enhancers	GM12878-XiMat	blood
18	chr5:127203000-127203400	Enhancers	Fetal Lung	lung
19	chr5:127203000-127203400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr5:127203000-127204000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:127203000-127204000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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