Variant report

Variant	rs3130670
Chromosome Location	chr6:30743864-30743865
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30742016..30748001-chr6:30748066..30750476,5	MCF-7	breast:
2	chr6:30648927..30651629-chr6:30742930..30745365,2	K562	blood:
3	chr6:30742999..30744721-chr6:30782116..30783840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228022	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1059612	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1264351	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1264361	0.85[EUR][1000 genomes]
rs1264373	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2524266	0.81[EUR][1000 genomes]
rs3094118	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3095276	0.83[AMR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3095334	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3095338	0.85[AMR][1000 genomes]
rs3129972	0.85[EUR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3129977	0.94[EUR][1000 genomes]
rs3129978	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3129980	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129982	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129983	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129984	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129985	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3130247	0.83[AMR][1000 genomes]
rs3130641	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130665	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130668	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130669	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130673	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3131041	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3131044	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131045	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131047	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131048	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131049	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131050	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131052	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3131054	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3131055	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131058	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131060	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132599	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3132600	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3132603	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3132605	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs886424	0.85[EUR][1000 genomes]
rs886425	0.85[EUR][1000 genomes]
rs9262130	0.83[AMR][1000 genomes]
rs9262132	0.83[AMR][1000 genomes]
rs9262141	0.83[AMR][1000 genomes]
rs9262142	0.83[AMR][1000 genomes]
rs9262146	0.83[AMR][1000 genomes]
rs9262174	0.85[AMR][1000 genomes]
rs9262200	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9262202	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9262203	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9262204	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	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
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv884104	chr6:30740680-30753146	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130670	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30734800-30747400	Weak transcription	Liver	Liver
2	chr6:30737600-30744200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:30737600-30746000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:30737600-30746000	Weak transcription	Fetal Lung	lung
5	chr6:30737600-30746000	Weak transcription	Gastric	stomach
6	chr6:30737600-30746000	Weak transcription	Lung	lung
7	chr6:30737600-30746000	Weak transcription	Pancreas	Pancrea
8	chr6:30737600-30746000	Weak transcription	Right Atrium	heart
9	chr6:30737600-30746000	Weak transcription	Right Ventricle	heart
10	chr6:30737600-30746000	Weak transcription	Spleen	Spleen
11	chr6:30737600-30746200	Weak transcription	Psoas Muscle	Psoas
12	chr6:30737600-30746600	Weak transcription	Aorta	Aorta
13	chr6:30737600-30749200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:30738000-30746000	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:30738000-30746400	Weak transcription	Esophagus	oesophagus
16	chr6:30738200-30745200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:30738400-30747000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:30738600-30745800	Weak transcription	NH-A	brain
19	chr6:30738600-30746000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:30738600-30746000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:30738600-30747000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:30738600-30749200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:30738800-30744600	Weak transcription	Fetal Thymus	thymus
24	chr6:30738800-30746200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:30738800-30746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:30739000-30744000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:30739000-30744200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:30739000-30746000	Weak transcription	K562	blood
29	chr6:30740600-30746000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:30740800-30744400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:30741000-30746000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:30741000-30749600	Weak transcription	Thymus	Thymus
33	chr6:30742000-30749000	Enhancers	HepG2	liver
34	chr6:30742200-30744400	Weak transcription	Primary T cells from cord blood	blood
35	chr6:30742200-30744800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:30742200-30746200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:30742400-30746200	Enhancers	Hela-S3	cervix
38	chr6:30742600-30747400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:30742800-30745600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:30742800-30746200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:30743000-30746200	Weak transcription	HSMMtube	muscle
42	chr6:30743200-30745400	Weak transcription	Fetal Muscle Leg	muscle
43	chr6:30743200-30745800	Weak transcription	NHDF-Ad	bronchial
44	chr6:30743200-30746000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:30743200-30746000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:30743200-30746000	Weak transcription	Placenta	Placenta
47	chr6:30743200-30746000	Weak transcription	Left Ventricle	heart
48	chr6:30743200-30746000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:30743200-30746000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:30743200-30746200	Weak transcription	HSMM	muscle

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