Variant report

Variant	rs474353
Chromosome Location	chr6:33229971-33229972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs120626	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071888	0.80[ASN][1000 genomes]
rs213199	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213201	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213202	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213204	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213206	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213216	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3135409	0.80[ASN][1000 genomes]
rs446735	0.93[ASN][1000 genomes]
rs456261	0.87[ASN][1000 genomes]
rs457565	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs463260	0.93[ASN][1000 genomes]
rs464865	0.93[ASN][1000 genomes]
rs469064	0.91[ASN][1000 genomes]
rs576890	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9277962	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv462893	chr6:33142539-33256471	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv602830	chr6:33142539-33256471	Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
4	nsv462894	chr6:33174783-33254665	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
5	nsv602831	chr6:33174783-33254665	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs474353	HLA-DPA1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33217400-33234200	Weak transcription	Small Intestine	intestine
2	chr6:33217800-33231200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:33217800-33231200	Weak transcription	Aorta	Aorta
4	chr6:33217800-33231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33218000-33231200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:33218000-33231200	Weak transcription	Gastric	stomach
7	chr6:33218000-33231400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:33218000-33231600	Weak transcription	Psoas Muscle	Psoas
9	chr6:33218000-33235400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:33218000-33238800	Weak transcription	Right Atrium	heart
11	chr6:33218200-33231800	Weak transcription	Fetal Brain Male	brain
12	chr6:33218400-33231200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:33218400-33231400	Weak transcription	Stomach Mucosa	stomach
14	chr6:33218400-33234200	Weak transcription	Fetal Heart	heart
15	chr6:33218600-33231200	Weak transcription	A549	lung
16	chr6:33218600-33231400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:33218600-33231600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:33218600-33233200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:33218600-33234200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:33218800-33230600	Weak transcription	Right Ventricle	heart
21	chr6:33218800-33232000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:33218800-33235400	Weak transcription	HUVEC	blood vessel
23	chr6:33219800-33230400	Weak transcription	Colonic Mucosa	Colon
24	chr6:33219800-33231200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:33220000-33230200	Weak transcription	Fetal Kidney	kidney
26	chr6:33220000-33231200	Weak transcription	HSMMtube	muscle
27	chr6:33220000-33231400	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:33223800-33237600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:33224400-33237400	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:33224400-33237600	Strong transcription	Thymus	Thymus
31	chr6:33224600-33237800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:33224600-33237800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr6:33224600-33238000	Strong transcription	Fetal Stomach	stomach
34	chr6:33224800-33235200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr6:33224800-33237600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:33224800-33237800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:33224800-33237800	Strong transcription	Fetal Thymus	thymus
38	chr6:33224800-33238000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:33225000-33237600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:33225000-33237600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:33225000-33237600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:33225000-33237600	Strong transcription	Liver	Liver
43	chr6:33225000-33238000	Strong transcription	Fetal Lung	lung
44	chr6:33225000-33238200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:33225200-33235200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr6:33225200-33237400	Strong transcription	Primary T cells from cord blood	blood
47	chr6:33225200-33237600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:33225200-33237800	Strong transcription	Adipose Nuclei	Adipose
49	chr6:33225400-33236600	Strong transcription	Dnd41	blood
50	chr6:33225400-33237200	Strong transcription	Rectal Mucosa Donor 29	rectum

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