Variant report

Variant	rs3130673
Chromosome Location	chr6:30746519-30746520
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30746284-30746892	U87	brain:	n/a	n/a
2	CHD1	chr6:30746278-30750816	IMR90	lung:	n/a	n/a
3	POLR2A	chr6:30746355-30746936	U87	brain:	n/a	n/a
4	GATA3	chr6:30746507-30746897	T-47D	breast:	n/a	n/a
5	POLR2A	chr6:30746517-30746819	U87	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30745917..30748118-chr6:30776110..30778177,2	K562	blood:
2	chr6:30742016..30748001-chr6:30748066..30750476,5	MCF-7	breast:
3	chr6:30746239..30748056-chr6:30850531..30852565,3	MCF-7	breast:
4	chr6:30694210..30695985-chr6:30745346..30747310,2	K562	blood:
5	chr6:30725912..30728357-chr6:30744418..30747133,2	K562	blood:
6	chr6:30710424..30713995-chr6:30746295..30752430,9	K562	blood:

No data

Variant related genes	Relation type
HCG20	TF binding region
ENSG00000272273	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000228022	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1059612	0.85[EUR][1000 genomes]
rs1264351	0.85[EUR][1000 genomes]
rs1264361	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264373	0.85[EUR][1000 genomes]
rs2524266	0.85[EUR][1000 genomes]
rs3094118	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3094125	0.83[EUR][1000 genomes]
rs3095326	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095328	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3095332	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3095334	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095338	0.93[AMR][1000 genomes]
rs3129972	0.89[EUR][1000 genomes]
rs3129973	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129974	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3129977	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3129978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129980	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129981	1.00[ASN][1000 genomes]
rs3129982	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129983	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129984	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129985	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130641	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130658	0.83[EUR][1000 genomes]
rs3130660	0.83[EUR][1000 genomes]
rs3130665	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130668	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130669	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130670	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3131041	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131044	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131045	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131047	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131048	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131049	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131050	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131052	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3131054	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3131055	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131058	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131060	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132583	0.83[EUR][1000 genomes]
rs3132585	0.83[EUR][1000 genomes]
rs3132599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132600	0.95[EUR][1000 genomes]
rs3132603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132605	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
rs886424	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886425	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262126	0.82[EUR][1000 genomes]
rs9262130	0.82[EUR][1000 genomes]
rs9262132	0.82[EUR][1000 genomes]
rs9262135	0.82[EUR][1000 genomes]
rs9262174	0.93[AMR][1000 genomes]
rs9262200	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262202	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262203	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262204	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3130673	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3130673	HIST1H2BM	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30734800-30747400	Weak transcription	Liver	Liver
2	chr6:30737600-30746600	Weak transcription	Aorta	Aorta
3	chr6:30737600-30749200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:30738400-30747000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:30738600-30747000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:30738600-30749200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr6:30738800-30746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:30741000-30749600	Weak transcription	Thymus	Thymus
9	chr6:30742000-30749000	Enhancers	HepG2	liver
10	chr6:30742600-30747400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:30743200-30747600	Weak transcription	HMEC	breast
12	chr6:30743400-30747000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:30743400-30747000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:30743600-30746800	Weak transcription	NHEK	skin
15	chr6:30744000-30758000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:30744200-30747000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:30744200-30747000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr6:30744200-30748000	Enhancers	Fetal Intestine Small	intestine
19	chr6:30744200-30749200	Enhancers	Fetal Heart	heart
20	chr6:30744200-30749200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:30744400-30747800	Enhancers	Fetal Intestine Large	intestine
22	chr6:30744400-30748200	Enhancers	Primary T cells from cord blood	blood
23	chr6:30744400-30748400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:30744600-30748600	Enhancers	Fetal Thymus	thymus
25	chr6:30744800-30749400	Enhancers	Stomach Mucosa	stomach
26	chr6:30745000-30748400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:30745400-30749600	Enhancers	Fetal Muscle Leg	muscle
28	chr6:30745600-30749400	Enhancers	Fetal Muscle Trunk	muscle
29	chr6:30745800-30747000	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr6:30745800-30747000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr6:30745800-30747400	Enhancers	Brain Anterior Caudate	brain
32	chr6:30745800-30747400	Enhancers	Duodenum Mucosa	Duodenum
33	chr6:30745800-30747800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr6:30745800-30749000	Enhancers	NHDF-Ad	bronchial
35	chr6:30745800-30749200	Enhancers	NH-A	brain
36	chr6:30746000-30746600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr6:30746000-30746600	Enhancers	Brain Substantia Nigra	brain
38	chr6:30746000-30746600	Enhancers	Rectal Smooth Muscle	rectum
39	chr6:30746000-30746800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:30746000-30746800	Enhancers	Brain Hippocampus Middle	brain
41	chr6:30746000-30746800	Enhancers	Gastric	stomach
42	chr6:30746000-30746800	Enhancers	Right Ventricle	heart
43	chr6:30746000-30747000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:30746000-30747000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:30746000-30747000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:30746000-30747000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:30746000-30747000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr6:30746000-30747000	Enhancers	Adipose Nuclei	Adipose
49	chr6:30746000-30747000	Enhancers	Fetal Lung	lung
50	chr6:30746000-30747000	Enhancers	Skeletal Muscle Female	skeletal muscle

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