Variant report

Variant	rs916438
Chromosome Location	chr1:169499659-169499660
allele	A/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 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	chr1:169475721..169488506-chr1:169493331..169501885,21	MCF-7	breast:
6	chr1:169452411..169456753-chr1:169494976..169501006,10	MCF-7	breast:
7	chr1:169480009..169482936-chr1:169495810..169499823,3	K562	blood:
8	chr1:169454264..169456422-chr1:169495447..169500944,4	K562	blood:
9	chr1:169454448..169456119-chr1:169499444..169502094,2	K562	blood:

No data

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

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1046712	0.93[ASN][1000 genomes]
rs10800454	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10800456	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1557570	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1557572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1894694	0.90[ASN][1000 genomes]
rs2157581	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298909	0.87[CEU][hapmap]
rs2301515	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820060	0.96[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs4656185	0.83[EUR][1000 genomes]
rs4656687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6021	0.82[CEU][hapmap]
rs6030	0.96[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs61805767	1.00[ASN][1000 genomes]
rs6686805	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6701330	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7535409	0.84[EUR][1000 genomes]
rs9332627	0.83[CEU][hapmap]
rs9332655	0.91[CEU][hapmap]
rs9332665	0.95[CEU][hapmap];0.84[EUR][1000 genomes]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs916438	SELL	cis	cerebellum	SCAN
rs916438	C1orf129	cis	cerebellum	SCAN
rs916438	XCL2	cis	cerebellum	SCAN
rs916438	C1orf112	cis	parietal	SCAN
rs916438	RXRG	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

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	chr1:169496000-169515200	Strong transcription	Liver	Liver
8	chr1:169496800-169500000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:169497200-169500000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:169497600-169499800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:169498200-169500000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:169498400-169499800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:169498400-169524000	Weak transcription	Placenta	Placenta
14	chr1:169498600-169500200	Enhancers	HSMMtube	muscle
15	chr1:169498600-169506200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:169498600-169507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:169498800-169501600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:169499000-169500000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:169499000-169500000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:169499000-169500000	Weak transcription	HSMM	muscle
21	chr1:169499000-169500200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:169499000-169500200	Enhancers	HMEC	breast
23	chr1:169499000-169500200	Enhancers	NHEK	skin
24	chr1:169499000-169500600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr1:169499000-169501800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:169499000-169504200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:169499000-169508400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:169499000-169519000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:169499200-169500000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:169499200-169500200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr1:169499200-169500200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:169499600-169500000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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