Variant report

Variant	rs6793061
Chromosome Location	chr3:151079960-151079961
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151074684..151076586-chr3:151078527..151080909,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1125541	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11708287	0.89[JPT][hapmap]
rs11715892	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717634	0.84[EUR][1000 genomes]
rs12487835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492699	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12494865	0.85[CEU][hapmap]
rs1352886	0.89[CEU][hapmap]
rs1388627	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1388628	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16863323	0.85[CEU][hapmap]
rs16863334	0.90[CEU][hapmap]
rs16863336	0.90[CEU][hapmap]
rs3971192	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4076581	0.81[CEU][hapmap]
rs41399847	0.82[JPT][hapmap]
rs4679794	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6793061	GPR171	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151063800-151099800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:151064400-151089200	Weak transcription	NHLF	lung
3	chr3:151064600-151112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:151065600-151109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:151065600-151115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:151065800-151082200	Weak transcription	Fetal Thymus	thymus
7	chr3:151067800-151083600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:151068000-151082600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:151069400-151129800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:151070400-151082800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:151072400-151080200	Weak transcription	Placenta	Placenta
12	chr3:151072400-151089800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:151072400-151091400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:151072600-151099800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:151074200-151082800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:151074200-151083800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:151074200-151084000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:151075200-151082800	Weak transcription	Pancreas	Pancrea
19	chr3:151075200-151084000	Weak transcription	Gastric	stomach
20	chr3:151075400-151099800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:151075600-151080000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:151075600-151080400	Weak transcription	Osteobl	bone
23	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
24	chr3:151075800-151084600	Weak transcription	Dnd41	blood
25	chr3:151075800-151091200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:151075800-151101200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:151075800-151101400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:151076000-151081000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:151076000-151083600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:151077200-151081200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:151078800-151080200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:151078800-151083400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:151079400-151082000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:151079400-151082400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr3:151079400-151082400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr3:151079600-151080000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:151079600-151080200	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:151079600-151080400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:151079600-151081400	Enhancers	Adipose Nuclei	Adipose
40	chr3:151079800-151080400	Genic enhancers	Brain Anterior Caudate	brain
41	chr3:151079800-151080400	Enhancers	HSMMtube	muscle
42	chr3:151079800-151080600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:151079800-151081000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:151079800-151082800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:151079800-151083000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:151079800-151105400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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