Variant report

Variant	rs11072478
Chromosome Location	chr15:74615507-74615508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74243196..74243740-chr15:74614599..74615555,2	K562	blood:
2	chr15:74614889..74615521-chr3:120277797..120278349,2	MCF-7	breast:
3	chr15:74419576..74420529-chr15:74614579..74615595,4	K562	blood:
4	chr15:74614136..74616902-chr15:74617695..74620669,2	K562	blood:
5	chr15:74346287..74347045-chr15:74614632..74615538,3	MCF-7	breast:
6	chr15:74423851..74425420-chr15:74614158..74616775,2	K562	blood:
7	chr15:74346094..74347046-chr15:74614640..74615508,4	K562	blood:

Variant related genes	Relation type
ENSG00000167178	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11632698	0.82[CEU][hapmap]
rs11634685	0.83[MEX][hapmap]
rs11638442	0.82[CEU][hapmap]
rs12438594	0.82[YRI][hapmap]
rs12440952	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12905100	0.81[CEU][hapmap]
rs12914852	0.81[EUR][1000 genomes]
rs12916123	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1484216	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1564782	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1564783	0.82[CEU][hapmap]
rs1843090	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1843091	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2277601	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2277602	0.88[CEU][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2277605	0.83[EUR][1000 genomes]
rs2277606	0.88[EUR][1000 genomes]
rs2279356	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2279357	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2279378	0.88[MEX][hapmap]
rs2415239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930291	0.82[CEU][hapmap];0.92[MEX][hapmap];0.80[EUR][1000 genomes]
rs2930300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930301	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2930302	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2930304	0.88[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2930306	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2959002	0.81[EUR][1000 genomes]
rs2959004	0.94[ASW][hapmap];0.88[CEU][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2959005	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2959006	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2959007	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2959008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2959011	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs351184	0.83[MEX][hapmap]
rs3825944	0.88[ASW][hapmap];0.82[YRI][hapmap]
rs4077581	0.88[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs4077582	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4077584	0.82[YRI][hapmap]
rs4598865	0.88[ASW][hapmap];0.82[YRI][hapmap]
rs4887135	0.82[CEU][hapmap]
rs6495096	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs68021814	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7174179	0.84[CEU][hapmap]
rs733434	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs751527	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs751528	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8031424	0.87[CEU][hapmap]
rs900799	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs900800	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs900802	0.89[ASW][hapmap];0.84[CEU][hapmap];0.85[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][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	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11072478	RPLP1	cis	parietal	SCAN
rs11072478	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74604800-74623400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr15:74611000-74617200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:74612000-74657800	Weak transcription	Right Atrium	heart
4	chr15:74612800-74617400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:74612800-74618600	Weak transcription	Ovary	ovary
6	chr15:74613000-74618800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:74613200-74617600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:74613200-74617600	Weak transcription	Fetal Thymus	thymus
9	chr15:74613200-74619000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:74613200-74619000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:74613400-74618800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:74613400-74618800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:74613400-74618800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:74613400-74619200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:74614200-74615800	Enhancers	Placenta	Placenta
16	chr15:74614400-74615600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:74614600-74615600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:74614800-74615600	Enhancers	Spleen	Spleen
19	chr15:74615200-74615600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:74615400-74615600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:74615400-74615600	Enhancers	Hela-S3	cervix
22	chr15:74615400-74619000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:74615400-74619000	Weak transcription	H1 Cell Line	embryonic stem cell

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