Variant report

Variant	rs120626
Chromosome Location	chr6:33247875-33247876
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33214775..33224346-chr6:33236521..33248678,40	K562	blood:
2	chr6:32935752..32938246-chr6:33246522..33249779,4	K562	blood:
3	chr6:33247491..33248418-chr6:33312501..33313418,4	MCF-7	breast:
4	chr6:33243392..33248315-chr6:33357393..33361975,11	K562	blood:
5	chr6:33242863..33248981-chr6:33374531..33379553,10	MCF-7	breast:
6	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
7	chr6:33247323..33248523-chr6:33266702..33268847,13	MCF-7	breast:
8	chr6:33174484..33176596-chr6:33246131..33248374,2	K562	blood:
9	chr6:33165702..33182742-chr6:33234718..33250379,54	K562	blood:
10	chr6:33247615..33248459-chr6:33266877..33268073,5	K562	blood:
11	chr6:32936522..32939181-chr6:33247297..33249779,3	K562	blood:
12	chr6:33247489..33248030-chr6:33280167..33280902,2	MCF-7	breast:
13	chr6:33247510..33248332-chr6:33265026..33265888,2	MCF-7	breast:
14	chr6:33237328..33248026-chr6:33370896..33379989,29	K562	blood:
15	chr6:33244680..33251060-chr6:33375427..33382644,12	MCF-7	breast:
16	chr6:33241747..33248128-chr6:33380775..33386072,13	K562	blood:
17	chr6:33242542..33249529-chr6:33381747..33388277,18	K562	blood:
18	chr6:33162573..33165564-chr6:33247072..33249621,2	K562	blood:
19	chr6:32939326..32941038-chr6:33246903..33249950,3	MCF-7	breast:
20	chr6:33247444..33248283-chr6:33393491..33394336,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000223837	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000202441	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2071888	0.83[ASN][1000 genomes]
rs213199	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213201	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213202	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213204	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213206	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213216	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3135408	0.82[ASN][1000 genomes]
rs3135409	0.83[ASN][1000 genomes]
rs446735	0.96[ASN][1000 genomes]
rs456261	0.89[ASN][1000 genomes]
rs457565	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs463260	0.96[ASN][1000 genomes]
rs464865	0.96[ASN][1000 genomes]
rs469064	0.94[ASN][1000 genomes]
rs474353	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576890	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9277962	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	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
8	nsv970109	chr6:33241506-33248502	Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs120626	HLA-DPA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33240600-33248800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:33241800-33248800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:33244800-33249200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:33245200-33248200	Weak transcription	HSMMtube	muscle
5	chr6:33245400-33248800	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr6:33245600-33249400	Strong transcription	HMEC	breast
7	chr6:33245600-33250400	Strong transcription	NHLF	lung
8	chr6:33245600-33251400	Weak transcription	NHDF-Ad	bronchial
9	chr6:33245600-33255200	Strong transcription	NHEK	skin
10	chr6:33245600-33255400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:33245800-33248000	Weak transcription	K562	blood
12	chr6:33245800-33248600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:33245800-33248800	Genic enhancers	Spleen	Spleen
14	chr6:33245800-33250400	Weak transcription	HUVEC	blood vessel
15	chr6:33245800-33254400	Weak transcription	Fetal Kidney	kidney
16	chr6:33245800-33255600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:33245800-33255800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:33245800-33255800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:33245800-33256000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:33245800-33256000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:33245800-33256400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr6:33246000-33248000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:33246000-33248000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:33246000-33248200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:33246000-33249800	Weak transcription	NH-A	brain
26	chr6:33246000-33251800	Weak transcription	Small Intestine	intestine
27	chr6:33246000-33252600	Weak transcription	Psoas Muscle	Psoas
28	chr6:33246000-33255200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:33246000-33255600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:33246000-33255600	Strong transcription	Fetal Intestine Large	intestine
31	chr6:33246000-33255800	Strong transcription	Fetal Stomach	stomach
32	chr6:33246000-33255800	Weak transcription	Right Atrium	heart
33	chr6:33246200-33248200	Genic enhancers	Primary monocytes fromperipheralblood	blood
34	chr6:33246200-33248200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
35	chr6:33246200-33248400	Genic enhancers	Rectal Mucosa Donor 29	rectum
36	chr6:33246200-33248600	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr6:33246200-33248600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:33246200-33248800	Strong transcription	Right Ventricle	heart
39	chr6:33246200-33249200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:33246200-33250000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:33246200-33251400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr6:33246200-33252600	Strong transcription	Fetal Brain Female	brain
43	chr6:33246200-33253000	Strong transcription	Dnd41	blood
44	chr6:33246200-33255000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:33246200-33255800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:33246200-33255800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:33246200-33255800	Strong transcription	Brain Anterior Caudate	brain
48	chr6:33246400-33248000	Genic enhancers	Adipose Nuclei	Adipose
49	chr6:33246400-33248000	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr6:33246400-33248400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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