Variant report

Variant	rs453590
Chromosome Location	chr6:33403422-33403423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33398677..33403495-chr6:33419995..33423723,6	K562	blood:
2	chr6:33243319..33245902-chr6:33402453..33405933,3	K562	blood:
3	chr6:33402335..33405767-chr6:33416394..33418965,3	MCF-7	breast:
4	chr6:33244202..33245902-chr6:33402963..33405933,2	K562	blood:

Variant related genes	Relation type
ENSG00000231500	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000235863	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11757273	0.82[ASN][1000 genomes]
rs1613451	0.82[ASN][1000 genomes]
rs1755045	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1755046	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1755047	0.82[ASN][1000 genomes]
rs1755048	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1755049	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076775	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs211456	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247385	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274730	0.81[ASN][1000 genomes]
rs2480487	0.80[ASN][1000 genomes]
rs2747477	0.90[ASN][1000 genomes]
rs2747479	0.90[ASN][1000 genomes]
rs2772373	0.83[ASN][1000 genomes]
rs2772375	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2772376	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2772387	0.80[ASN][1000 genomes]
rs2772389	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2772390	0.80[ASN][1000 genomes]
rs2772391	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2772392	0.81[ASN][1000 genomes]
rs3130025	0.80[ASN][1000 genomes]
rs411136	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461964	0.81[ASN][1000 genomes]
rs465223	0.81[ASN][1000 genomes]
rs465506	0.81[ASN][1000 genomes]
rs4711325	0.95[ASN][1000 genomes]
rs4713625	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66840884	0.81[ASN][1000 genomes]
rs7382303	0.89[ASN][1000 genomes]
rs9357159	0.81[ASN][1000 genomes]
rs9366822	0.80[ASN][1000 genomes]
rs9380355	0.81[ASN][1000 genomes]
rs9461856	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1019212	chr6:33398031-33413930	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs453590	TAF11	cis	cerebellum	SCAN
rs453590	SPDEF	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33396400-33405200	Weak transcription	Psoas Muscle	Psoas
2	chr6:33396600-33416000	Weak transcription	Pancreas	Pancrea
3	chr6:33399200-33403600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:33399400-33421200	Weak transcription	HMEC	breast
5	chr6:33399400-33421600	Weak transcription	Stomach Mucosa	stomach
6	chr6:33399600-33403600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:33399600-33409200	Weak transcription	Small Intestine	intestine
8	chr6:33399600-33421400	Weak transcription	HUVEC	blood vessel
9	chr6:33399800-33421400	Weak transcription	A549	lung
10	chr6:33400000-33412800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:33400000-33418000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:33400000-33420600	Strong transcription	Brain Germinal Matrix	brain
13	chr6:33400400-33406000	Weak transcription	Fetal Brain Male	brain
14	chr6:33400800-33406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:33400800-33412800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:33401000-33404600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:33401000-33406000	Weak transcription	GM12878-XiMat	blood
18	chr6:33401200-33420800	Strong transcription	Fetal Brain Female	brain
19	chr6:33401400-33404600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr6:33401400-33406400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:33401400-33417600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr6:33401400-33418800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:33401400-33421400	Weak transcription	Right Atrium	heart
24	chr6:33401600-33416600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:33402000-33404800	Weak transcription	Right Ventricle	heart
26	chr6:33402000-33417600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:33402000-33418000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:33402000-33418000	Strong transcription	NHLF	lung
29	chr6:33402000-33418200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:33402000-33420600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:33402200-33404200	Weak transcription	NH-A	brain
32	chr6:33402200-33405400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:33402200-33405400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:33402200-33407600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:33402200-33417400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:33402200-33417400	Strong transcription	Thymus	Thymus
37	chr6:33402200-33418200	Strong transcription	Fetal Muscle Leg	muscle
38	chr6:33402200-33418600	Strong transcription	Dnd41	blood
39	chr6:33402200-33420000	Strong transcription	Fetal Thymus	thymus
40	chr6:33402200-33420800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:33402400-33420800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:33402600-33404200	Weak transcription	Left Ventricle	heart
43	chr6:33402600-33417600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:33402600-33420000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:33402600-33420400	Strong transcription	Fetal Stomach	stomach
46	chr6:33402600-33421400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:33402800-33406400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:33402800-33406600	Strong transcription	Esophagus	oesophagus
49	chr6:33402800-33406800	Strong transcription	Lung	lung
50	chr6:33402800-33407200	Strong transcription	Fetal Lung	lung

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