Variant report

Variant	rs6030
Chromosome Location	chr1:169498975-169498976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169447411..169449419-chr1:169497697..169499792,2	MCF-7	breast:
2	chr1:169478952..169480932-chr1:169498032..169500995,2	MCF-7	breast:
3	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
4	chr1:169490192..169493609-chr1:169495804..169500257,7	MCF-7	breast:
5	chr1:169485353..169488291-chr1:169497708..169499497,2	K562	blood:
6	chr1:169475721..169488506-chr1:169493331..169501885,21	MCF-7	breast:
7	chr1:169464842..169466756-chr1:169497919..169499478,2	MCF-7	breast:
8	chr1:169452411..169456753-chr1:169494976..169501006,10	MCF-7	breast:
9	chr1:169480009..169482936-chr1:169495810..169499823,3	K562	blood:
10	chr1:169454264..169456422-chr1:169495447..169500944,4	K562	blood:
11	chr1:169461099..169462759-chr1:169496804..169499532,2	MCF-7	breast:
12	chr1:169486560..169487382-chr1:169498336..169499053,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198734	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10800454	0.87[EUR][1000 genomes]
rs10800456	0.83[CEU][hapmap]
rs1121789	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[YRI][hapmap]
rs1557570	0.95[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1557572	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2157581	0.89[EUR][1000 genomes]
rs2187952	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs2187953	0.90[AFR][1000 genomes]
rs2213866	0.82[AFR][1000 genomes]
rs2213867	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs2227244	0.83[CEU][hapmap];0.84[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs2239851	0.81[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap]
rs2239852	0.96[CEU][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs2298909	0.82[CEU][hapmap]
rs2301515	0.96[CEU][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2420373	0.88[AFR][1000 genomes]
rs3766109	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs3820060	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4524	0.81[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.81[GIH][hapmap]
rs4525	0.81[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap]
rs4656185	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656187	0.83[CEU][hapmap];0.92[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs4656685	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap]
rs4656687	0.96[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs6016	0.92[CHB][hapmap];0.84[GIH][hapmap]
rs6017	0.81[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap]
rs6021	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs6032	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs6662593	0.93[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap]
rs6670393	0.83[AFR][1000 genomes]
rs6686805	0.86[EUR][1000 genomes]
rs6701330	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7535409	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs916438	0.96[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs9332599	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332600	0.81[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap]
rs9332619	0.93[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs9332620	0.93[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs9332627	0.87[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap];0.93[MKK][hapmap]
rs9332635	0.81[CHB][hapmap]
rs9332643	0.87[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.81[GIH][hapmap];0.93[MKK][hapmap]
rs9332651	0.81[AFR][1000 genomes]
rs9332653	0.84[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs9332655	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs9332665	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9332667	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs970741	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap];0.82[MKK][hapmap]
rs974793	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872533	chr1:169490401-169508576	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Uric acid levels	23703922	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6030	RXRG	cis	parietal	SCAN
rs6030	XCL2	cis	cerebellum	SCAN
rs6030	SELL	cis	cerebellum	SCAN
rs6030	C1orf129	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169484800-169501000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:169485400-169510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:169487400-169501000	Weak transcription	Right Ventricle	heart
4	chr1:169491600-169500800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:169492000-169499800	Weak transcription	Left Ventricle	heart
6	chr1:169494000-169502800	Strong transcription	HepG2	liver
7	chr1:169494800-169499200	Enhancers	Stomach Mucosa	stomach
8	chr1:169496000-169499200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:169496000-169515200	Strong transcription	Liver	Liver
10	chr1:169496200-169499000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:169496200-169499000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr1:169496400-169499000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
13	chr1:169496800-169500000	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:169497000-169499000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:169497000-169499000	Enhancers	Fetal Thymus	thymus
16	chr1:169497200-169499200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:169497200-169499400	Enhancers	Fetal Intestine Large	intestine
18	chr1:169497200-169499600	Enhancers	Dnd41	blood
19	chr1:169497200-169500000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:169497600-169499800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:169498000-169499000	Flanking Active TSS	NHEK	skin
22	chr1:169498200-169499000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr1:169498200-169499000	Enhancers	HSMM	muscle
24	chr1:169498200-169499200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:169498200-169499200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr1:169498200-169499200	Enhancers	Hela-S3	cervix
27	chr1:169498200-169500000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:169498400-169499000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:169498400-169499000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:169498400-169499000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:169498400-169499000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:169498400-169499000	Enhancers	NH-A	brain
33	chr1:169498400-169499200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:169498400-169499600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:169498400-169499600	Enhancers	Fetal Intestine Small	intestine
36	chr1:169498400-169499800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:169498400-169524000	Weak transcription	Placenta	Placenta
38	chr1:169498600-169499000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:169498600-169499000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:169498600-169499000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:169498600-169499000	Flanking Active TSS	HMEC	breast
42	chr1:169498600-169499400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr1:169498600-169500200	Enhancers	HSMMtube	muscle
44	chr1:169498600-169506200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:169498600-169507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:169498800-169499000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr1:169498800-169499000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:169498800-169499000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:169498800-169499000	Enhancers	Duodenum Mucosa	Duodenum
50	chr1:169498800-169499000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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