Variant report

Variant	rs213202
Chromosome Location	chr6:33232055-33232056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33231663-33232153	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:33231378-33232239	K562	blood:	n/a	n/a
3	POLR2A	chr6:33231813-33232134	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:33232021-33232219	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:33231848-33232125	K562	blood:	n/a	n/a
6	POLR2A	chr6:33231124-33233532	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:33231796-33232332	K562	blood:	n/a	n/a
8	POLR2A	chr6:33231786-33232104	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:33231542-33232379	K562	blood:	n/a	n/a
10	POLR2A	chr6:33231644-33232178	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:33231918-33232090	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:33231547-33232145	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:33231783-33232281	K562	blood:	n/a	n/a
14	POLR2A	chr6:33231565-33232169	HL-60	blood:	n/a	n/a
15	POLR2A	chr6:33231988-33232157	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33164650..33184503-chr6:33230350..33245922,64	K562	blood:
2	chr6:33217011..33220390-chr6:33230294..33232709,3	K562	blood:
3	chr6:33174850..33176996-chr6:33230833..33233131,2	K562	blood:
4	chr6:33216736..33218315-chr6:33231569..33233281,2	MCF-7	breast:

No data

Variant related genes	Relation type
VPS52	TF binding region
ENSG00000112473	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000225463	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000204228	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs120626	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071888	0.80[ASN][1000 genomes]
rs213199	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213201	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213204	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213206	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213216	0.87[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	0.87[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]
rs474353	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576890	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9277962	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv5249	chr6:33231743-33249478	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs213202	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	chr6:33218000-33235400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:33218000-33238800	Weak transcription	Right Atrium	heart
4	chr6:33218400-33234200	Weak transcription	Fetal Heart	heart
5	chr6:33218600-33233200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:33218600-33234200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:33218800-33235400	Weak transcription	HUVEC	blood vessel
8	chr6:33223800-33237600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:33224400-33237400	Strong transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:33224400-33237600	Strong transcription	Thymus	Thymus
11	chr6:33224600-33237800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:33224600-33237800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr6:33224600-33238000	Strong transcription	Fetal Stomach	stomach
14	chr6:33224800-33235200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr6:33224800-33237600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:33224800-33237800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:33224800-33237800	Strong transcription	Fetal Thymus	thymus
18	chr6:33224800-33238000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:33225000-33237600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:33225000-33237600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:33225000-33237600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:33225000-33237600	Strong transcription	Liver	Liver
23	chr6:33225000-33238000	Strong transcription	Fetal Lung	lung
24	chr6:33225000-33238200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:33225200-33235200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr6:33225200-33237400	Strong transcription	Primary T cells from cord blood	blood
27	chr6:33225200-33237600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:33225200-33237800	Strong transcription	Adipose Nuclei	Adipose
29	chr6:33225400-33236600	Strong transcription	Dnd41	blood
30	chr6:33225400-33237200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr6:33225400-33237800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr6:33225800-33234400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:33225800-33237800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:33226000-33236800	Strong transcription	Rectal Smooth Muscle	rectum
35	chr6:33226200-33237600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:33226200-33237600	Strong transcription	Fetal Intestine Large	intestine
37	chr6:33226600-33237200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:33226600-33237400	Strong transcription	Brain Substantia Nigra	brain
39	chr6:33226600-33237600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr6:33226600-33237800	Strong transcription	Brain Hippocampus Middle	brain
41	chr6:33226800-33232600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:33226800-33237400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:33226800-33237800	Strong transcription	Placenta	Placenta
44	chr6:33227000-33238000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:33227600-33237400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:33227800-33238000	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:33227800-33238200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:33228000-33237000	Strong transcription	Fetal Brain Female	brain
49	chr6:33228000-33238800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:33228200-33237800	Strong transcription	Brain Inferior Temporal Lobe	brain

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