Variant report

Variant	rs6485774
Chromosome Location	chr11:47773226-47773227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47772614..47775136-chr11:47775998..47778043,4	K562	blood:
2	chr11:47772614..47774288-chr11:47775998..47777897,2	K562	blood:
3	chr11:47760881..47762523-chr11:47771591..47773857,2	MCF-7	breast:
4	chr11:47771480..47774571-chr11:47789058..47790932,3	MCF-7	breast:
5	chr11:47772681..47775102-chr11:47787112..47788847,2	K562	blood:
6	chr11:47772923..47774749-chr11:47778974..47781299,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109920	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10742816	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs10742820	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs11039387	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11819979	0.97[ASN][1000 genomes]
rs11820480	1.00[ASN][1000 genomes]
rs12421563	0.81[AFR][1000 genomes]
rs1474056	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs17791016	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1872167	0.88[ASN][1000 genomes]
rs2138767	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2290851	0.80[YRI][hapmap]
rs2305982	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2305983	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2869531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2869532	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4147730	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs4303192	0.82[ASN][1000 genomes]
rs4752786	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4752791	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4752796	0.80[YRI][hapmap]
rs4752865	0.80[YRI][hapmap];0.80[AFR][1000 genomes]
rs4752871	0.95[ASN][1000 genomes]
rs4752872	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4752877	0.92[ASN][1000 genomes]
rs4752879	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57436966	0.95[ASN][1000 genomes]
rs58357937	0.91[ASN][1000 genomes]
rs59205786	0.97[ASN][1000 genomes]
rs60515486	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485772	0.90[ASN][1000 genomes]
rs6485783	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6485784	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6485788	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7101582	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7116299	0.82[ASN][1000 genomes]
rs7120737	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7121264	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7122217	0.82[AFR][1000 genomes]
rs7124949	0.95[ASN][1000 genomes]
rs7924699	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7927611	0.95[ASN][1000 genomes]
rs7931089	0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7942031	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7945911	0.86[ASN][1000 genomes]
rs7952204	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6485774	ATG13	cis	parietal	SCAN
rs6485774	LOC441601	cis	cerebellum	SCAN
rs6485774	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47737000-47786200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:47737200-47779800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:47737600-47779200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47737800-47776400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr11:47737800-47776600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:47737800-47776600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:47737800-47777200	Strong transcription	NH-A	brain
8	chr11:47737800-47782800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr11:47737800-47785800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:47737800-47786000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:47737800-47786200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:47737800-47786200	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr11:47737800-47786400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:47737800-47786400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:47737800-47786400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:47737800-47786400	Strong transcription	Fetal Thymus	thymus
17	chr11:47737800-47786800	Strong transcription	Placenta	Placenta
18	chr11:47738000-47776200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:47738000-47776200	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr11:47738000-47776400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:47738000-47776600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr11:47738000-47786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:47738000-47786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:47738000-47786400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr11:47738000-47786800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:47738200-47776200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr11:47738200-47776600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:47738200-47779000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:47738200-47786400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:47738400-47776600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr11:47738400-47786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:47738600-47785800	Strong transcription	Dnd41	blood
33	chr11:47739800-47776800	Strong transcription	Thymus	Thymus
34	chr11:47742800-47776400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:47742800-47776400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr11:47743000-47776400	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:47743800-47776200	Strong transcription	Primary T cells from cord blood	blood
38	chr11:47746000-47777600	Strong transcription	Fetal Muscle Leg	muscle
39	chr11:47746200-47776200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:47746200-47776400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr11:47746200-47776800	Strong transcription	Left Ventricle	heart
42	chr11:47746200-47778200	Strong transcription	Osteobl	bone
43	chr11:47746200-47786000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:47746400-47786200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr11:47746800-47776000	Strong transcription	Hela-S3	cervix
46	chr11:47747400-47786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:47747600-47786400	Strong transcription	Fetal Intestine Large	intestine
48	chr11:47747800-47776600	Strong transcription	Adipose Nuclei	Adipose
49	chr11:47747800-47786200	Strong transcription	A549	lung
50	chr11:47748000-47786000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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