Variant report

Variant	rs3131060
Chromosome Location	chr6:30763291-30763292
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30707638..30712527-chr6:30761800..30767458,10	K562	blood:
2	chr6:30758839..30761709-chr6:30762940..30765835,2	MCF-7	breast:
3	chr6:30747273..30752496-chr6:30759061..30765017,9	K562	blood:
4	chr6:30705811..30713504-chr6:30753060..30768565,33	MCF-7	breast:
5	chr6:30748485..30750756-chr6:30762000..30763594,2	MCF-7	breast:
6	chr6:30757280..30759870-chr6:30760366..30765437,6	K562	blood:
7	chr6:30760214..30763491-chr6:30779624..30782451,3	K562	blood:
8	chr6:30762133..30768787-chr6:30785989..30790050,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272273	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000137312	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1049633	0.80[EUR][1000 genomes]
rs1264308	0.80[EUR][1000 genomes]
rs1264325	0.80[EUR][1000 genomes]
rs1264347	0.80[EUR][1000 genomes]
rs1264351	0.88[EUR][1000 genomes]
rs1264361	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264373	0.88[EUR][1000 genomes]
rs2263298	0.82[EUR][1000 genomes]
rs2517578	0.80[EUR][1000 genomes]
rs2524266	0.88[EUR][1000 genomes]
rs2535328	0.80[EUR][1000 genomes]
rs2535332	0.80[EUR][1000 genomes]
rs2535334	0.80[EUR][1000 genomes]
rs2535340	0.80[EUR][1000 genomes]
rs2844656	0.80[EUR][1000 genomes]
rs3094088	0.80[EUR][1000 genomes]
rs3094118	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3095326	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3095328	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3095332	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3095334	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095338	0.93[AMR][1000 genomes]
rs3129972	0.80[EUR][1000 genomes]
rs3129973	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129974	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129977	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129978	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129980	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129981	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129982	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129983	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129984	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130641	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130665	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130668	0.84[AMR][1000 genomes]
rs3130669	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130670	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3130673	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131041	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131044	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131045	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131047	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131048	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131049	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131050	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131052	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3131054	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131055	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131058	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132577	0.80[EUR][1000 genomes]
rs3132599	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132600	0.86[EUR][1000 genomes]
rs3132603	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3132605	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55694686	1.00[ASN][1000 genomes]
rs55702639	1.00[ASN][1000 genomes]
rs55707154	1.00[ASN][1000 genomes]
rs55848160	1.00[ASN][1000 genomes]
rs56051116	1.00[ASN][1000 genomes]
rs56105977	1.00[ASN][1000 genomes]
rs56123606	1.00[ASN][1000 genomes]
rs56133130	1.00[ASN][1000 genomes]
rs56377503	1.00[ASN][1000 genomes]
rs56804692	1.00[ASN][1000 genomes]
rs886422	0.80[EUR][1000 genomes]
rs886424	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886425	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262174	0.93[AMR][1000 genomes]
rs9262200	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262202	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262203	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262204	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv1023695	chr6:30754540-30773349	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3131060	VARSL	cis	multi-tissue	Pritchard
rs3131060	HLA-H	cis	multi-tissue	Pritchard
rs3131060	HLA-G	cis	multi-tissue	Pritchard
rs3131060	HLA-C	cis	multi-tissue	Pritchard
rs3131060	HLA-A	cis	brain	seeQTL
rs3131060	HLA-DQB1	cis	multi-tissue	Pritchard
rs3131060	HLA-A	cis	multi-tissue	Pritchard
rs3131060	BTN3A2	cis	multi-tissue	Pritchard
rs3131060	HLA-DRB1	cis	multi-tissue	Pritchard
rs3131060	HLA-DQA1	cis	multi-tissue	Pritchard
rs3131060	HIST1H2BM	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30751000-30769800	Weak transcription	Right Ventricle	heart
2	chr6:30757000-30763400	Weak transcription	NHEK	skin
3	chr6:30757400-30763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:30757600-30763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:30757600-30768400	Weak transcription	Hela-S3	cervix
6	chr6:30758000-30765600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:30758400-30764200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr6:30759200-30768800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:30760600-30764400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr6:30761600-30764200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:30761600-30781000	Weak transcription	Small Intestine	intestine
12	chr6:30761800-30763800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:30761800-30764200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:30761800-30772000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr6:30762000-30764000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:30762000-30764200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:30762000-30764200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr6:30762000-30764400	Enhancers	K562	blood
19	chr6:30762000-30766200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:30762000-30766800	Weak transcription	HUVEC	blood vessel
21	chr6:30762000-30768600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:30762400-30766200	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:30762400-30766800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:30762600-30766200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:30762600-30766200	Weak transcription	Fetal Lung	lung
26	chr6:30762600-30766200	Weak transcription	NHLF	lung
27	chr6:30762600-30767000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:30762600-30768800	Weak transcription	Fetal Stomach	stomach
29	chr6:30762800-30763600	Weak transcription	GM12878-XiMat	blood
30	chr6:30762800-30763600	Weak transcription	HepG2	liver
31	chr6:30762800-30763800	Weak transcription	Primary B cells from cord blood	blood
32	chr6:30763000-30763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:30763000-30763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:30763000-30763600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:30763000-30764000	Weak transcription	Primary T cells from cord blood	blood
36	chr6:30763000-30765800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:30763000-30766800	Weak transcription	Placenta	Placenta
38	chr6:30763200-30768600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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