Variant report

Variant	rs12026423
Chromosome Location	chr1:114078037-114078038
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	chr1:114072573..114074275-chr1:114076748..114078498,2	MCF-7	breast:
2	chr1:114056876..114059527-chr1:114077132..114079049,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10858003	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10858004	0.87[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs10858006	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102660	0.89[TSI][hapmap]
rs11102667	0.80[ASN][1000 genomes]
rs1146183	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1146184	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1146185	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12065882	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1217194	0.80[ASN][1000 genomes]
rs1217202	0.92[ASN][1000 genomes]
rs1217212	0.90[ASN][1000 genomes]
rs1217224	0.90[ASN][1000 genomes]
rs1217229	0.92[ASN][1000 genomes]
rs1217238	0.98[ASN][1000 genomes]
rs1230673	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1235000	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.92[ASN][1000 genomes]
rs1237290	0.92[ASN][1000 genomes]
rs12757859	0.84[ASN][1000 genomes]
rs1343630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13524	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1624335	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1743594	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1743595	0.90[ASN][1000 genomes]
rs1777239	0.86[ASN][1000 genomes]
rs2636003	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2798137	0.84[ASN][1000 genomes]
rs7515189	0.86[TSI][hapmap]
rs7518766	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429525	0.86[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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv437013	chr1:114065955-114129092	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12026423	BCL2L15	cis	cerebellum	SCAN
rs12026423	DENND2C	cis	parietal	SCAN
rs12026423	GADD45A	trans	lymphoblastoid	seeQTL
rs12026423	SIKE1	cis	parietal	SCAN
rs12026423	PHTF1	cis	parietal	SCAN
rs12026423	MAGI3	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114071000-114079800	Weak transcription	A549	lung
2	chr1:114072200-114095800	Weak transcription	Aorta	Aorta
3	chr1:114076000-114079800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:114076600-114078600	Enhancers	HSMMtube	muscle
5	chr1:114076600-114078800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:114076600-114079200	Enhancers	NHEK	skin
7	chr1:114076600-114079400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:114076600-114080000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:114076800-114078200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:114076800-114079400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:114077200-114079000	Weak transcription	NHLF	lung
12	chr1:114077200-114079800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:114077200-114079800	Weak transcription	Ovary	ovary
14	chr1:114077200-114081800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:114077200-114082600	Weak transcription	Fetal Intestine Large	intestine
16	chr1:114077200-114082800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:114077400-114079400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:114077400-114080400	Enhancers	NHDF-Ad	bronchial
19	chr1:114077600-114083000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:114077800-114078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:114077800-114079800	Weak transcription	Pancreas	Pancrea
22	chr1:114077800-114080800	Weak transcription	Psoas Muscle	Psoas
23	chr1:114077800-114082400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:114077800-114082600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:114077800-114083000	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:114077800-114084400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:114077800-114084400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:114077800-114084400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:114078000-114078400	Weak transcription	NH-A	brain
30	chr1:114078000-114078400	Weak transcription	Osteobl	bone
31	chr1:114078000-114090000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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