Variant report

Variant	rs6887565
Chromosome Location	chr5:112586122-112586123
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112585167..112587277-chr5:112587981..112591044,3	MCF-7	breast:

Extended variants
information (count: 126 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10519343	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10519345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10519346	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10900685	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1116547	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11241197	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs11241201	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11241206	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs11738075	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11738215	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs11740045	0.95[ASN][1000 genomes]
rs11740190	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11740233	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11740318	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11740353	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11740443	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11741794	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs11741937	0.95[ASN][1000 genomes]
rs11741963	0.81[EUR][1000 genomes]
rs11743052	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];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11744606	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]
rs11746532	0.95[ASN][1000 genomes]
rs11746791	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11746821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11748058	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11748465	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[ASN][1000 genomes]
rs11748524	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[ASN][1000 genomes]
rs11749864	0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs11750945	0.82[CEU][hapmap]
rs12186466	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12188069	0.90[ASW][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12188070	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12188230	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12516418	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs12518849	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];0.97[ASN][1000 genomes]
rs12519753	0.82[EUR][1000 genomes]
rs12520003	1.00[CHB][hapmap]
rs12521391	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs12522862	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs12523027	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs12523255	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12523284	0.95[ASN][1000 genomes]
rs1517209	0.81[EUR][1000 genomes]
rs1586943	0.81[EUR][1000 genomes]
rs17135454	0.90[CHD][hapmap]
rs17135463	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs17135488	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];0.97[ASN][1000 genomes]
rs17135506	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17135507	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17135514	0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17135515	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17135517	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17135519	0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17135520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17135526	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.97[ASN][1000 genomes]
rs17135531	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs17135534	0.86[MEX][hapmap]
rs17135535	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs17135543	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs17135546	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs17135597	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs17135608	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17135616	0.90[CEU][hapmap]
rs17135630	0.92[CEU][hapmap]
rs1845289	0.95[ASN][1000 genomes]
rs1997521	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2068923	0.95[MEX][hapmap]
rs2091803	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs2091804	0.90[ASN][1000 genomes]
rs34271294	0.87[ASN][1000 genomes]
rs3846721	0.92[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs4632792	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4705806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705810	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4705811	0.81[ASN][1000 genomes]
rs4705814	0.92[CEU][hapmap]
rs4705817	0.83[CEU][hapmap]
rs4705818	0.81[EUR][1000 genomes]
rs56294433	0.87[ASN][1000 genomes]
rs56362568	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59107004	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59222257	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60087454	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60437559	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6594695	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6594696	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6594697	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs66644309	0.81[EUR][1000 genomes]
rs66893265	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67063423	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67373655	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67550282	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67764628	0.81[EUR][1000 genomes]
rs68069850	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6864528	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs6877524	0.90[MEX][hapmap]
rs6879761	0.95[ASN][1000 genomes]
rs6879800	0.92[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs6888602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244768	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs73244769	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs73244770	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73244772	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73244779	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73246604	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73246629	0.95[ASN][1000 genomes]
rs73246648	0.92[ASN][1000 genomes]
rs73246657	0.87[ASN][1000 genomes]
rs73246677	0.95[ASN][1000 genomes]
rs73246681	0.95[ASN][1000 genomes]
rs7707127	1.00[YRI][hapmap]
rs7717000	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7724707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7724717	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];0.95[ASN][1000 genomes]
rs7724936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs971370	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs971371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs971373	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs977997	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs9800316	0.81[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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6887565	MCC	cis	parietal	SCAN
rs6887565	DCP2	cis	lymphoblastoid	seeQTL
rs6887565	YTHDC2	cis	cerebellum	SCAN
rs6887565	DCP2	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112572400-112590400	Weak transcription	Liver	Liver
2	chr5:112579600-112587000	Weak transcription	Aorta	Aorta
3	chr5:112580600-112597400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:112581400-112590800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:112582200-112586400	Weak transcription	HMEC	breast
6	chr5:112582800-112586400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:112582800-112586400	Weak transcription	NHEK	skin
8	chr5:112582800-112601000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:112583000-112586200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:112583000-112586400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:112583000-112604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:112583200-112586400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:112583200-112587000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:112583600-112599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:112583800-112587000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:112583800-112588000	Enhancers	Fetal Heart	heart
17	chr5:112584400-112586400	Enhancers	Stomach Smooth Muscle	stomach
18	chr5:112584400-112587400	Enhancers	NH-A	brain
19	chr5:112584400-112587400	Enhancers	Osteobl	bone
20	chr5:112584800-112586200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:112584800-112586800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:112585000-112587000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr5:112585000-112589000	Enhancers	Right Ventricle	heart
24	chr5:112585000-112589400	Enhancers	Ovary	ovary
25	chr5:112585200-112586600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:112585200-112586600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:112585200-112586600	Enhancers	Fetal Stomach	stomach
28	chr5:112585200-112587600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr5:112585200-112588000	Enhancers	HUVEC	blood vessel
30	chr5:112585200-112588200	Enhancers	Fetal Muscle Leg	muscle
31	chr5:112585200-112588400	Enhancers	Right Atrium	heart
32	chr5:112585200-112589400	Enhancers	Left Ventricle	heart
33	chr5:112585400-112586200	Enhancers	Psoas Muscle	Psoas
34	chr5:112585400-112586200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr5:112585400-112586200	Enhancers	Stomach Mucosa	stomach
36	chr5:112585400-112586800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr5:112585400-112586800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:112585400-112586800	Enhancers	Fetal Kidney	kidney
39	chr5:112585400-112587200	Enhancers	NHDF-Ad	bronchial
40	chr5:112585400-112588000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr5:112585600-112586200	Enhancers	HSMM	muscle
42	chr5:112585600-112586400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:112585600-112586400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:112585600-112588200	Enhancers	Adipose Nuclei	Adipose
45	chr5:112585800-112586200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:112585800-112586200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:112585800-112586400	Enhancers	HSMMtube	muscle
48	chr5:112585800-112586600	Enhancers	Brain Anterior Caudate	brain
49	chr5:112585800-112586600	Enhancers	Pancreas	Pancrea
50	chr5:112585800-112587000	Enhancers	NHLF	lung

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