Variant report

Variant	rs932460
Chromosome Location	chr20:11331894-11331895
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:11330194..11333067-chr20:11363546..11365974,2	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10432736	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10485747	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107551	0.88[ASN][1000 genomes]
rs11087022	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11087023	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11697289	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11697845	0.83[ASN][1000 genomes]
rs11698552	0.83[ASN][1000 genomes]
rs12625544	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12625567	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1883970	0.83[ASN][1000 genomes]
rs1997878	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2103762	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2143872	0.82[ASN][1000 genomes]
rs2143874	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2223861	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2327377	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2327379	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327403	0.83[ASN][1000 genomes]
rs28374547	0.82[ASN][1000 genomes]
rs35418295	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35742586	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35961934	0.90[ASN][1000 genomes]
rs4347904	0.83[ASN][1000 genomes]
rs4359714	0.83[ASN][1000 genomes]
rs4440032	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4449203	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4468879	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4473452	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473453	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485619	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4491786	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528833	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4538269	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4541301	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4564855	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586703	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4813054	0.83[ASN][1000 genomes]
rs4813055	0.83[ASN][1000 genomes]
rs4813056	0.83[ASN][1000 genomes]
rs4813986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813987	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4813988	0.83[ASN][1000 genomes]
rs4813989	0.83[ASN][1000 genomes]
rs4813990	0.83[ASN][1000 genomes]
rs4813991	0.83[ASN][1000 genomes]
rs59242255	0.82[ASN][1000 genomes]
rs6033108	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033110	0.80[ASN][1000 genomes]
rs6033119	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033120	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033121	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6040563	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040568	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040569	0.84[ASN][1000 genomes]
rs6040571	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040572	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040575	0.81[ASN][1000 genomes]
rs6040577	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6040578	0.83[ASN][1000 genomes]
rs6040582	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6040583	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6040587	0.88[EUR][1000 genomes]
rs6040591	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6040592	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6104740	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6108922	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6108923	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6108927	0.84[ASN][1000 genomes]
rs6108929	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131193	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6131194	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6131195	0.83[ASN][1000 genomes]
rs6131196	0.83[ASN][1000 genomes]
rs6131197	0.83[ASN][1000 genomes]
rs6131199	0.83[ASN][1000 genomes]
rs6131200	0.81[ASN][1000 genomes]
rs6134181	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6134190	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134191	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134192	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134198	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134204	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134205	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134212	0.83[ASN][1000 genomes]
rs6134215	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134216	0.83[ASN][1000 genomes]
rs6134217	0.83[ASN][1000 genomes]
rs6134219	0.83[ASN][1000 genomes]
rs6134220	0.83[ASN][1000 genomes]
rs6134221	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134223	0.90[ASN][1000 genomes]
rs62191844	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62193969	0.83[ASN][1000 genomes]
rs68130714	0.83[ASN][1000 genomes]
rs714655	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs715370	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715371	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715372	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742822	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8114418	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8119263	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8119401	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs932460	HAO1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11329000-11332000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:11330400-11332000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:11330400-11332400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:11330400-11332600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr20:11330600-11332200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:11330600-11332400	Enhancers	HMEC	breast
7	chr20:11330600-11333400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:11330600-11334400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr20:11330800-11332000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr20:11330800-11332400	Enhancers	Brain Substantia Nigra	brain
11	chr20:11330800-11333200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:11330800-11333600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr20:11330800-11334200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr20:11330800-11336200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:11331000-11332400	Enhancers	Psoas Muscle	Psoas
16	chr20:11331000-11333000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr20:11331000-11338400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr20:11331200-11332200	Enhancers	Brain Hippocampus Middle	brain
19	chr20:11331200-11332400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr20:11331200-11332800	Enhancers	Fetal Intestine Small	intestine
21	chr20:11331200-11333200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr20:11331200-11333800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr20:11331400-11332000	Weak transcription	Brain Anterior Caudate	brain
24	chr20:11331400-11332200	Enhancers	NHEK	skin
25	chr20:11331400-11333400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:11331600-11333000	Weak transcription	Fetal Lung	lung
27	chr20:11331800-11332200	Active TSS	Brain Germinal Matrix	brain
28	chr20:11331800-11332200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr20:11331800-11332200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr20:11331800-11333200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr20:11331800-11333400	Enhancers	HUES64 Cell Line	embryonic stem cell

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