Variant report

Variant	rs316013
Chromosome Location	chr6:160672625-160672626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:160670882..160673777-chr6:160676211..160678542,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2448295	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2450975	0.86[GIH][hapmap]
rs2619270	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2774230	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2774232	0.92[EUR][1000 genomes]
rs2928034	0.82[AMR][1000 genomes]
rs2928036	0.86[EUR][1000 genomes]
rs315979	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315980	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs315981	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315982	0.87[EUR][1000 genomes]
rs315983	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs315984	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315985	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315987	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315988	0.81[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315989	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315990	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315993	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315994	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs315995	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316000	0.86[GIH][hapmap]
rs316003	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316004	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs316005	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316006	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs316007	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs316008	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs316011	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316012	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316015	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316016	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316018	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316021	0.83[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs316022	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34360089	0.93[EUR][1000 genomes]
rs479078	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs515140	0.88[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs543435	0.83[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs582158	0.92[EUR][1000 genomes]
rs617217	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs625438	0.92[EUR][1000 genomes]
rs638360	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs657051	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9457875	0.90[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9457878	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1030746	chr6:160592321-160867031	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538493	chr6:160592321-160867031	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030171	chr6:160648469-161091864	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv886809	chr6:160670494-160979275	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs316013	MAS1	cis	cerebellum	SCAN
rs316013	QKI	cis	cerebellum	SCAN
rs316013	RSPH3	cis	cerebellum	SCAN
rs316013	WTAP	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160667800-160674200	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr6:160668000-160674600	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr6:160669200-160673600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:160669400-160673200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:160669400-160674400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:160669600-160674400	Weak transcription	Fetal Intestine Small	intestine
7	chr6:160669600-160679000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:160670000-160678200	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:160670200-160676000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:160670400-160673400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:160670400-160675600	Weak transcription	NHEK	skin
12	chr6:160670600-160674200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:160670800-160673800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:160671000-160674600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:160671200-160672800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:160671200-160673400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:160671200-160673600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:160671200-160674400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr6:160671600-160672800	Enhancers	A549	lung
20	chr6:160671600-160675000	Enhancers	H9 Cell Line	embryonic stem cell
21	chr6:160671600-160675600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:160672000-160674800	Weak transcription	Fetal Kidney	kidney
23	chr6:160672400-160673400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:160672400-160673600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:160672600-160673000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:160672600-160673600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:160672600-160673800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:160672600-160674000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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