Variant report

Variant	rs3132600
Chromosome Location	chr6:30746367-30746368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 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

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
ENSG00000204580	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1049633	0.81[EUR][1000 genomes]
rs1059612	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1264308	0.81[EUR][1000 genomes]
rs1264325	0.81[EUR][1000 genomes]
rs1264347	0.81[EUR][1000 genomes]
rs1264351	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1264361	0.85[EUR][1000 genomes]
rs1264373	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2263298	0.83[EUR][1000 genomes]
rs2517578	0.81[EUR][1000 genomes]
rs2524266	0.89[EUR][1000 genomes]
rs2535328	0.81[EUR][1000 genomes]
rs2535332	0.81[EUR][1000 genomes]
rs2535334	0.81[EUR][1000 genomes]
rs2535340	0.81[EUR][1000 genomes]
rs2844656	0.81[EUR][1000 genomes]
rs3094088	0.81[EUR][1000 genomes]
rs3094118	0.94[EUR][1000 genomes]
rs3094125	0.87[EUR][1000 genomes]
rs3095276	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3095327	0.81[EUR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095334	0.95[EUR][1000 genomes]
rs3129972	0.93[EUR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3129977	0.94[EUR][1000 genomes]
rs3129978	0.95[EUR][1000 genomes]
rs3129980	0.86[EUR][1000 genomes]
rs3129982	0.86[EUR][1000 genomes]
rs3129983	0.86[EUR][1000 genomes]
rs3129984	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3129985	0.86[EUR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes]
rs3130641	0.89[EUR][1000 genomes]
rs3130658	0.87[EUR][1000 genomes]
rs3130660	0.87[EUR][1000 genomes]
rs3130665	0.94[EUR][1000 genomes]
rs3130668	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130669	0.84[EUR][1000 genomes]
rs3130670	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3130673	0.95[EUR][1000 genomes]
rs3131041	0.91[EUR][1000 genomes]
rs3131044	0.86[EUR][1000 genomes]
rs3131045	0.86[EUR][1000 genomes]
rs3131047	0.86[EUR][1000 genomes]
rs3131048	0.83[EUR][1000 genomes]
rs3131049	0.86[EUR][1000 genomes]
rs3131050	0.86[EUR][1000 genomes]
rs3131052	0.91[EUR][1000 genomes]
rs3131054	0.81[EUR][1000 genomes]
rs3131055	0.86[EUR][1000 genomes]
rs3131058	0.86[EUR][1000 genomes]
rs3131060	0.86[EUR][1000 genomes]
rs3132577	0.81[EUR][1000 genomes]
rs3132582	0.81[EUR][1000 genomes]
rs3132583	0.87[EUR][1000 genomes]
rs3132585	0.87[EUR][1000 genomes]
rs3132599	0.95[EUR][1000 genomes]
rs3132603	0.95[EUR][1000 genomes]
rs3132605	0.95[EUR][1000 genomes]
rs886422	0.81[EUR][1000 genomes]
rs886424	0.85[EUR][1000 genomes]
rs886425	0.85[EUR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262130	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262132	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262141	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262142	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262143	0.83[EUR][1000 genomes]
rs9262146	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262200	0.86[EUR][1000 genomes]
rs9262202	0.86[EUR][1000 genomes]
rs9262204	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
rs3132600	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 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	chr6:30738000-30746400	Weak transcription	Esophagus	oesophagus
5	chr6:30738400-30747000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:30738600-30747000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:30738600-30749200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:30738800-30746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:30741000-30749600	Weak transcription	Thymus	Thymus
10	chr6:30742000-30749000	Enhancers	HepG2	liver
11	chr6:30742600-30747400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:30743200-30747600	Weak transcription	HMEC	breast
13	chr6:30743400-30747000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:30743400-30747000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:30743600-30746800	Weak transcription	NHEK	skin
16	chr6:30744000-30758000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:30744200-30747000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr6:30744200-30747000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr6:30744200-30748000	Enhancers	Fetal Intestine Small	intestine
20	chr6:30744200-30749200	Enhancers	Fetal Heart	heart
21	chr6:30744200-30749200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:30744400-30747800	Enhancers	Fetal Intestine Large	intestine
23	chr6:30744400-30748200	Enhancers	Primary T cells from cord blood	blood
24	chr6:30744400-30748400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:30744600-30748600	Enhancers	Fetal Thymus	thymus
26	chr6:30744800-30749400	Enhancers	Stomach Mucosa	stomach
27	chr6:30745000-30748400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:30745400-30749600	Enhancers	Fetal Muscle Leg	muscle
29	chr6:30745600-30749400	Enhancers	Fetal Muscle Trunk	muscle
30	chr6:30745800-30747000	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr6:30745800-30747000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:30745800-30747400	Enhancers	Brain Anterior Caudate	brain
33	chr6:30745800-30747400	Enhancers	Duodenum Mucosa	Duodenum
34	chr6:30745800-30747800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr6:30745800-30749000	Enhancers	NHDF-Ad	bronchial
36	chr6:30745800-30749200	Enhancers	NH-A	brain
37	chr6:30746000-30746400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:30746000-30746400	Enhancers	Small Intestine	intestine
39	chr6:30746000-30746400	Flanking Active TSS	A549	lung
40	chr6:30746000-30746600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr6:30746000-30746600	Enhancers	Brain Substantia Nigra	brain
42	chr6:30746000-30746600	Enhancers	Rectal Smooth Muscle	rectum
43	chr6:30746000-30746800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:30746000-30746800	Enhancers	Brain Hippocampus Middle	brain
45	chr6:30746000-30746800	Enhancers	Gastric	stomach
46	chr6:30746000-30746800	Enhancers	Right Ventricle	heart
47	chr6:30746000-30747000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:30746000-30747000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:30746000-30747000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:30746000-30747000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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