Variant report

Variant	rs11696447
Chromosome Location	chr20:1406877-1406878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1405279..1407726-chr20:1449432..1451429,2	K562	blood:
2	chr20:1405728..1407229-chr20:1414214..1416774,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11699494	1.00[CHB][hapmap]
rs12481707	1.00[JPT][hapmap]
rs13163	1.00[CHB][hapmap]
rs1474879	1.00[ASN][1000 genomes]
rs1474880	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap]
rs16995310	1.00[CHB][hapmap]
rs16995332	1.00[CHB][hapmap]
rs17793360	1.00[JPT][hapmap]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884393	1.00[JPT][hapmap]
rs2064645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2064646	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2273321	1.00[JPT][hapmap]
rs2873522	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3829697	1.00[JPT][hapmap]
rs41308086	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814102	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs58194712	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58718584	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59239479	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6041689	1.00[CHB][hapmap]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042506	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042550	1.00[CHB][hapmap]
rs6042568	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042574	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042578	1.00[CHB][hapmap]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105140	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109437	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109511	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109522	1.00[CHB][hapmap]
rs6109740	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109784	1.00[CHB][hapmap]
rs6109837	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109838	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109962	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109986	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109989	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109992	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6110189	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110193	1.00[CHB][hapmap]
rs6514337	1.00[CHB][hapmap]
rs6514364	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs66497853	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7271240	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8117563	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8118276	1.00[CHB][hapmap]
rs8118710	1.00[JPT][hapmap]
rs8124855	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap]
rs959813	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs984497	1.00[JPT][hapmap]
rs984498	1.00[JPT][hapmap]

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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11696447	FKBP1A	cis	multi-tissue	Pritchard
rs11696447	SNRPB	cis	cerebellum	SCAN
rs11696447	TCF15	cis	cerebellum	SCAN
rs11696447	CDS2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr20:1400000-1408200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr20:1400000-1410600	Weak transcription	Osteobl	bone
4	chr20:1403200-1408000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr20:1404000-1409000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr20:1404600-1407200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
8	chr20:1404800-1407000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:1404800-1407800	Weak transcription	Primary T cells from cord blood	blood
10	chr20:1404800-1408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:1404800-1408200	Weak transcription	Fetal Intestine Large	intestine
12	chr20:1404800-1408200	Weak transcription	Lung	lung
13	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
14	chr20:1405000-1407000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr20:1405000-1407200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr20:1405000-1407800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr20:1405000-1408000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:1405000-1408200	Weak transcription	Adipose Nuclei	Adipose
19	chr20:1405000-1409600	Weak transcription	Stomach Mucosa	stomach
20	chr20:1405000-1414600	Weak transcription	Thymus	Thymus
21	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr20:1405200-1407000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr20:1405200-1407400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr20:1405200-1407800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr20:1405200-1408400	Weak transcription	K562	blood
26	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr20:1405400-1407200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr20:1405400-1407200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr20:1405400-1408000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
32	chr20:1405600-1408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:1405600-1409800	Weak transcription	HMEC	breast
34	chr20:1406000-1408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr20:1406000-1410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr20:1406200-1408200	Weak transcription	NHEK	skin
37	chr20:1406600-1409000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr20:1406600-1409000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr20:1406800-1408400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr20:1406800-1408600	Enhancers	Primary hematopoietic stem cells	blood
41	chr20:1406800-1408800	Enhancers	H1 Cell Line	embryonic stem cell
42	chr20:1406800-1409000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr20:1406800-1409000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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