Variant report

Variant	rs17508449
Chromosome Location	chr1:114085145-114085146
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	chr1:114084981..114088872-chr1:114091176..114094977,3	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1419231	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17274627	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs17359281	0.86[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs17461918	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2146018	0.81[ASN][1000 genomes]
rs3761934	0.81[ASN][1000 genomes]
rs41352847	0.81[ASN][1000 genomes]
rs4259646	0.80[CHD][hapmap]
rs4838993	0.86[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4838994	0.86[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4839000	0.86[CEU][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap]
rs4839327	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839329	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4839330	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4839331	0.86[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4839332	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4839333	0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap]
rs6537790	0.80[CHD][hapmap]
rs6678422	0.81[ASN][1000 genomes]
rs7514649	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7554019	0.80[CHD][hapmap]

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	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
2	nsv946153	chr1:114080236-114088844	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17508449	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs17508449	MAGI3	cis	multi-tissue	Pritchard
rs17508449	PTPN22	cis	multi-tissue	Pritchard
rs17508449	PHTF1	cis	lymphoblastoid	seeQTL
rs17508449	DCLRE1B	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114072200-114095800	Weak transcription	Aorta	Aorta
2	chr1:114078000-114090000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:114080600-114088600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:114082400-114088400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:114082600-114100400	Weak transcription	Fetal Kidney	kidney
6	chr1:114082800-114085600	Enhancers	HMEC	breast
7	chr1:114083200-114085600	Enhancers	NHDF-Ad	bronchial
8	chr1:114083200-114099800	Weak transcription	Pancreas	Pancrea
9	chr1:114083400-114095200	Weak transcription	Liver	Liver
10	chr1:114083400-114100000	Weak transcription	Ovary	ovary
11	chr1:114083400-114110000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:114083600-114085600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:114083800-114085400	Enhancers	A549	lung
14	chr1:114084000-114092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:114084200-114085600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:114084200-114088600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:114084400-114085200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:114084400-114085600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:114084400-114085600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:114084400-114085600	Enhancers	NHLF	lung
21	chr1:114084600-114085400	Enhancers	Gastric	stomach
22	chr1:114084600-114085400	Enhancers	HSMMtube	muscle
23	chr1:114084600-114085400	Enhancers	HUVEC	blood vessel
24	chr1:114084600-114085400	Flanking Active TSS	NHEK	skin
25	chr1:114084600-114085600	Weak transcription	HepG2	liver
26	chr1:114084600-114089800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:114084800-114085400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:114084800-114085400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:114084800-114085400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:114084800-114085600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:114084800-114095200	Weak transcription	Fetal Intestine Large	intestine
32	chr1:114084800-114095600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:114085000-114085400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:114085000-114085400	Flanking Active TSS	NH-A	brain
35	chr1:114085000-114085400	Flanking Active TSS	Osteobl	bone
36	chr1:114085000-114092400	Weak transcription	Fetal Intestine Small	intestine

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