Variant report

Variant	rs520605
Chromosome Location	chr1:184795779-184795780
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	chr1:184794140..184796874-chr1:184950845..184952866,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10797988	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs10797989	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1857954	0.87[EUR][1000 genomes]
rs2135737	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs338562	0.88[EUR][1000 genomes]
rs338566	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs338570	0.89[EUR][1000 genomes]
rs338572	0.87[ASN][1000 genomes]
rs4011648	0.89[EUR][1000 genomes]
rs4011650	0.89[EUR][1000 genomes]
rs4651234	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs481215	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs484847	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs512642	0.85[ASN][1000 genomes]
rs521366	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533853	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs539362	0.86[ASN][1000 genomes]
rs543912	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs549088	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs556163	0.88[ASN][1000 genomes]
rs595769	0.91[ASN][1000 genomes]
rs641337	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6424964	0.89[EUR][1000 genomes]
rs6671637	0.89[EUR][1000 genomes]
rs7519082	0.88[EUR][1000 genomes]
rs906285	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv508677	chr1:184778620-184825302	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs520605	PRG4	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184768000-184809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:184772400-184801800	Weak transcription	Primary T cells from cord blood	blood
3	chr1:184773200-184809400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:184775600-184796800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:184783000-184807800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:184783200-184796400	Weak transcription	NHLF	lung
7	chr1:184783200-184796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:184783200-184796800	Weak transcription	NHDF-Ad	bronchial
9	chr1:184783200-184809200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:184783400-184803200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:184785400-184801200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:184786000-184797800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:184786600-184796000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:184786600-184805200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:184787800-184796800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:184787800-184799000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:184788000-184797400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:184788200-184796200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:184788600-184796800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:184789800-184802000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:184790200-184809600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:184791000-184797000	Enhancers	Right Atrium	heart
23	chr1:184791600-184796800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:184791800-184796000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr1:184791800-184796800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:184792200-184795800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:184792200-184796400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:184792200-184796400	Weak transcription	Lung	lung
29	chr1:184792200-184799400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:184792200-184805200	Weak transcription	Fetal Intestine Small	intestine
31	chr1:184792400-184798600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:184792800-184796400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:184792800-184796800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:184792800-184805200	Weak transcription	Small Intestine	intestine
35	chr1:184792800-184810000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:184793000-184795800	Enhancers	Adipose Nuclei	Adipose
37	chr1:184793000-184796400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:184793000-184796400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:184793000-184796800	Weak transcription	Hela-S3	cervix
40	chr1:184793000-184796800	Weak transcription	NHEK	skin
41	chr1:184793000-184799000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:184793000-184805000	Weak transcription	K562	blood
43	chr1:184793000-184809600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:184793000-184813000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:184793200-184796800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:184793400-184797200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:184793400-184799000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:184793400-184809200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:184793600-184798200	Enhancers	Colon Smooth Muscle	Colon
50	chr1:184793600-184799400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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