Variant report

Variant	rs211456
Chromosome Location	chr6:33389381-33389382
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr6:33388925-33389451	PBDE	blood:	n/a	chr6:33389050-33389057 chr6:33389043-33389064 chr6:33389050-33389057 chr6:33389046-33389062 chr6:33389050-33389057 chr6:33389075-33389086 chr6:33389049-33389059 chr6:33389046-33389057

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr6:33385453..33389637-chr6:33419628..33424957,5	MCF-7	breast:
3	chr6:33242929..33245218-chr6:33388533..33390277,2	K562	blood:
4	chr6:33237639..33241732-chr6:33383253..33390116,11	K562	blood:
5	chr6:33357335..33362175-chr6:33383352..33389421,14	K562	blood:
6	chr6:33372672..33375320-chr6:33388854..33391700,2	MCF-7	breast:
7	chr6:33279097..33283546-chr6:33386045..33390564,5	MCF-7	breast:

Variant related genes	Relation type
CUTA	TF binding region
ENSG00000236104	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000231925	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1755045	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1755046	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1755048	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1755049	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076775	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247385	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2747477	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2747479	0.90[ASN][1000 genomes]
rs2772373	0.81[ASN][1000 genomes]
rs2772375	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2772376	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2772389	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2772391	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs411136	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs453590	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs461964	0.80[ASN][1000 genomes]
rs465223	0.80[ASN][1000 genomes]
rs465506	0.80[ASN][1000 genomes]
rs4711325	0.92[ASN][1000 genomes]
rs4713625	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7382303	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9461856	0.88[ASN][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	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	nsv932196	chr6:33383131-33400706	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
6	esv3491403	chr6:33386574-33390272	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
7	esv3491404	chr6:33386574-33390272	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv3325690	chr6:33386999-33389547	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	esv3404776	chr6:33387074-33389997	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs211456	HLA-DPA1	Cis_1M	lymphoblastoid	RTeQTL
rs211456	TAF11	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33386000-33392600	Weak transcription	Gastric	stomach
2	chr6:33386200-33389400	Flanking Active TSS	Dnd41	blood
3	chr6:33386800-33389800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr6:33386800-33392600	Weak transcription	Left Ventricle	heart
5	chr6:33387000-33392200	Weak transcription	Hela-S3	cervix
6	chr6:33387400-33389600	Active TSS	Brain Angular Gyrus	brain
7	chr6:33387400-33392200	Weak transcription	Placenta	Placenta
8	chr6:33387400-33392200	Weak transcription	Spleen	Spleen
9	chr6:33387600-33389400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr6:33387600-33392400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:33387800-33389400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:33387800-33389400	Active TSS	Brain Hippocampus Middle	brain
13	chr6:33387800-33389600	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:33387800-33391800	Weak transcription	Lung	lung
15	chr6:33387800-33392000	Weak transcription	Small Intestine	intestine
16	chr6:33387800-33392200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:33387800-33392200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:33387800-33392200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:33387800-33392200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:33387800-33392400	Weak transcription	Primary B cells from cord blood	blood
21	chr6:33387800-33392400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:33387800-33392400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:33387800-33392600	Weak transcription	A549	lung
24	chr6:33388000-33389400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:33388000-33392400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:33388000-33392400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:33388000-33392400	Weak transcription	Adipose Nuclei	Adipose
28	chr6:33388000-33392400	Weak transcription	Brain Substantia Nigra	brain
29	chr6:33388000-33392400	Weak transcription	HMEC	breast
30	chr6:33388000-33392600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:33388000-33392600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:33388000-33392600	Weak transcription	HSMM	muscle
33	chr6:33388200-33392200	Weak transcription	Psoas Muscle	Psoas
34	chr6:33388400-33389400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:33388400-33392000	Weak transcription	Colonic Mucosa	Colon
36	chr6:33388400-33392200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:33388400-33392200	Weak transcription	Aorta	Aorta
38	chr6:33388400-33392200	Weak transcription	Right Ventricle	heart
39	chr6:33388400-33392600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:33388400-33392600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:33388600-33389400	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr6:33388600-33389400	Enhancers	Fetal Stomach	stomach
43	chr6:33388600-33389600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:33388600-33389600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:33388600-33389600	Enhancers	NHDF-Ad	bronchial
46	chr6:33388600-33389800	Enhancers	Primary T cells from cord blood	blood
47	chr6:33388600-33389800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:33388600-33389800	Enhancers	Thymus	Thymus
49	chr6:33388600-33390200	Enhancers	Fetal Thymus	thymus
50	chr6:33388600-33391000	Weak transcription	Stomach Smooth Muscle	stomach

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