Variant report

Variant	rs3129984
Chromosome Location	chr6:30761572-30761573
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30760063..30761714-chr6:30779972..30782451,2	K562	blood:
2	chr6:30760005..30762685-chr6:30764182..30767386,3	K562	blood:
3	chr6:30758839..30761709-chr6:30762940..30765835,2	MCF-7	breast:
4	chr6:30747273..30752496-chr6:30759061..30765017,9	K562	blood:
5	chr6:30760005..30761677-chr6:30763965..30767626,3	K562	blood:
6	chr6:30705811..30713504-chr6:30753060..30768565,33	MCF-7	breast:
7	chr6:30757280..30759870-chr6:30760366..30765437,6	K562	blood:
8	chr6:30760214..30763491-chr6:30779624..30782451,3	K562	blood:
9	chr6:30761074..30762645-chr6:30772509..30774883,2	K562	blood:
10	chr6:30691897..30694851-chr6:30760025..30762962,2	K562	blood:
11	chr6:30736036..30738964-chr6:30760194..30762277,2	K562	blood:

No data

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

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1049633	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1059612	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1264308	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1264325	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1264347	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1264351	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1264361	0.91[EUR][1000 genomes]
rs1264373	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2263298	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2517578	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2524266	0.95[EUR][1000 genomes]
rs2535328	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2535332	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2535334	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2535340	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2844656	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2844661	0.86[EUR][1000 genomes]
rs3094088	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3094118	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3094125	0.81[EUR][1000 genomes]
rs3095156	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3095276	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3095326	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3095328	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095332	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095334	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129972	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129973	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3129974	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129977	0.88[EUR][1000 genomes]
rs3129978	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129980	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129982	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129983	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129985	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130641	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3130658	0.81[EUR][1000 genomes]
rs3130660	0.81[EUR][1000 genomes]
rs3130665	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130668	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3130669	0.84[AMR][1000 genomes]
rs3130670	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130673	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131041	0.94[EUR][1000 genomes]
rs3131044	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131045	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131047	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131048	0.88[EUR][1000 genomes]
rs3131049	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131050	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131052	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131054	0.87[EUR][1000 genomes]
rs3131055	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131058	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131060	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131781	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3132577	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132583	0.81[EUR][1000 genomes]
rs3132585	0.81[EUR][1000 genomes]
rs3132599	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132600	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132603	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132605	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132610	0.82[AMR][1000 genomes]
rs886422	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs886424	0.91[EUR][1000 genomes]
rs886425	0.91[EUR][1000 genomes]
rs9262126	0.81[AMR][1000 genomes]
rs9262130	0.91[AMR][1000 genomes]
rs9262132	0.91[AMR][1000 genomes]
rs9262135	0.81[AMR][1000 genomes]
rs9262141	0.91[AMR][1000 genomes]
rs9262142	0.91[AMR][1000 genomes]
rs9262146	0.91[AMR][1000 genomes]
rs9262200	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262202	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262203	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262204	0.84[AMR][1000 genomes];0.88[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3129984	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30750800-30761600	Weak transcription	NHDF-Ad	bronchial
2	chr6:30751000-30769800	Weak transcription	Right Ventricle	heart
3	chr6:30755800-30762600	Enhancers	Fetal Thymus	thymus
4	chr6:30756400-30761600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:30756400-30761600	Weak transcription	A549	lung
6	chr6:30756800-30761800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:30757000-30763400	Weak transcription	NHEK	skin
8	chr6:30757200-30761600	Weak transcription	Adipose Nuclei	Adipose
9	chr6:30757400-30763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:30757600-30762800	Enhancers	HepG2	liver
11	chr6:30757600-30763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:30757600-30768400	Weak transcription	Hela-S3	cervix
13	chr6:30758000-30765600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:30758400-30764200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:30759200-30768800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:30759800-30763000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:30760600-30762600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:30760600-30764400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:30760800-30762400	Enhancers	Fetal Muscle Leg	muscle
20	chr6:30761000-30761600	Enhancers	Primary B cells from cord blood	blood
21	chr6:30761000-30761800	Enhancers	Stomach Mucosa	stomach
22	chr6:30761000-30762600	Enhancers	Fetal Muscle Trunk	muscle
23	chr6:30761200-30761600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:30761200-30761600	Enhancers	Small Intestine	intestine
25	chr6:30761200-30761600	Enhancers	K562	blood
26	chr6:30761200-30761800	Enhancers	Fetal Intestine Large	intestine
27	chr6:30761200-30761800	Enhancers	Lung	lung
28	chr6:30761200-30761800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr6:30761200-30762000	Enhancers	Primary hematopoietic stem cells	blood
30	chr6:30761200-30762000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr6:30761200-30762000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr6:30761200-30762000	Enhancers	Thymus	Thymus
33	chr6:30761200-30762000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr6:30761200-30762600	Enhancers	Primary B cells from peripheral blood	blood
35	chr6:30761200-30762600	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr6:30761200-30762600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:30761200-30762600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr6:30761200-30762600	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr6:30761200-30763000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:30761400-30761600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:30761400-30761600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:30761400-30761600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:30761400-30761600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr6:30761400-30761600	Enhancers	Placenta	Placenta
45	chr6:30761400-30761800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:30761400-30761800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr6:30761400-30761800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr6:30761400-30761800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:30761400-30761800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:30761400-30761800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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