Variant report

Variant	rs2524266
Chromosome Location	chr6:30780568-30780569
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30780089..30782522-chr6:30839223..30841388,2	K562	blood:
2	chr6:30707810..30715390-chr6:30779530..30784762,15	K562	blood:
3	chr6:30748186..30751274-chr6:30779635..30781913,3	K562	blood:
4	chr6:30739130..30742242-chr6:30780166..30782431,3	K562	blood:
5	chr6:30775890..30781762-chr6:30785090..30789723,9	MCF-7	breast:
6	chr6:30766009..30775294-chr6:30775700..30782710,15	MCF-7	breast:
7	chr6:30739945..30741810-chr6:30780568..30783125,2	K562	blood:
8	chr6:30765847..30772235-chr6:30775518..30781372,10	K562	blood:
9	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
10	chr6:30696761..30700438-chr6:30779538..30781456,3	K562	blood:
11	chr6:30708338..30713459-chr6:30777538..30783709,13	K562	blood:
12	chr6:30779954..30784896-chr6:30785156..30789787,6	K562	blood:
13	chr6:30687466..30692169-chr6:30775918..30784078,7	K562	blood:
14	chr6:30760063..30761714-chr6:30779972..30782451,2	K562	blood:
15	chr6:30777633..30780399-chr6:30780437..30782571,2	MCF-7	breast:
16	chr6:30706744..30716171-chr6:30774931..30783832,28	MCF-7	breast:
17	chr6:30760214..30763491-chr6:30779624..30782451,3	K562	blood:
18	chr6:30779859..30782628-chr6:30850009..30853631,3	K562	blood:
19	chr6:30655802..30657936-chr6:30780184..30782576,2	K562	blood:
20	chr6:30716968..30722090-chr6:30774929..30783584,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272540	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000201988	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1049633	0.92[EUR][1000 genomes]
rs1059612	0.83[AMR][1000 genomes]
rs1264308	0.92[EUR][1000 genomes]
rs1264325	0.92[EUR][1000 genomes]
rs1264347	0.92[EUR][1000 genomes]
rs1264350	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1264351	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264361	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1264373	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2263298	0.93[EUR][1000 genomes]
rs2517578	0.92[EUR][1000 genomes]
rs2535328	0.92[EUR][1000 genomes]
rs2535332	0.92[EUR][1000 genomes]
rs2535334	0.92[EUR][1000 genomes]
rs2535340	0.92[EUR][1000 genomes]
rs2844656	0.92[EUR][1000 genomes]
rs2844661	0.90[EUR][1000 genomes]
rs3094088	0.92[EUR][1000 genomes]
rs3094118	0.83[EUR][1000 genomes]
rs3095156	0.89[EUR][1000 genomes]
rs3095326	0.86[EUR][1000 genomes]
rs3095328	0.87[EUR][1000 genomes]
rs3095332	0.87[EUR][1000 genomes]
rs3095334	0.85[EUR][1000 genomes]
rs3129972	0.82[EUR][1000 genomes]
rs3129973	0.86[EUR][1000 genomes]
rs3129974	0.87[EUR][1000 genomes]
rs3129977	0.83[EUR][1000 genomes]
rs3129978	0.85[EUR][1000 genomes]
rs3129980	0.88[EUR][1000 genomes]
rs3129982	0.88[EUR][1000 genomes]
rs3129983	0.88[EUR][1000 genomes]
rs3129984	0.95[EUR][1000 genomes]
rs3129985	0.88[EUR][1000 genomes]
rs3130641	0.91[EUR][1000 genomes]
rs3130665	0.83[EUR][1000 genomes]
rs3130670	0.81[EUR][1000 genomes]
rs3130673	0.85[EUR][1000 genomes]
rs3131041	0.89[EUR][1000 genomes]
rs3131044	0.88[EUR][1000 genomes]
rs3131045	0.88[EUR][1000 genomes]
rs3131047	0.88[EUR][1000 genomes]
rs3131048	0.84[EUR][1000 genomes]
rs3131049	0.88[EUR][1000 genomes]
rs3131050	0.88[EUR][1000 genomes]
rs3131052	0.89[EUR][1000 genomes]
rs3131054	0.83[EUR][1000 genomes]
rs3131055	0.88[EUR][1000 genomes]
rs3131058	0.88[EUR][1000 genomes]
rs3131060	0.88[EUR][1000 genomes]
rs3131781	0.85[EUR][1000 genomes]
rs3132577	0.92[EUR][1000 genomes]
rs3132599	0.85[EUR][1000 genomes]
rs3132600	0.89[EUR][1000 genomes]
rs3132603	0.85[EUR][1000 genomes]
rs3132605	0.85[EUR][1000 genomes]
rs886422	0.92[EUR][1000 genomes]
rs886424	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs886425	0.84[AFR][1000 genomes];0.95[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]
rs9262200	0.88[EUR][1000 genomes]
rs9262202	0.88[EUR][1000 genomes]
rs9262203	0.81[EUR][1000 genomes]
rs9262204	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv884105	chr6:30775579-30786676	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv884106	chr6:30775579-30787323	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv884107	chr6:30776483-30787323	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2524266	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	chr6:30761600-30781000	Weak transcription	Small Intestine	intestine
2	chr6:30767200-30781200	Weak transcription	Gastric	stomach
3	chr6:30776400-30783200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:30776400-30783400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr6:30776600-30783400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:30777200-30781000	Enhancers	K562	blood
7	chr6:30777200-30783200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr6:30778400-30781000	Enhancers	Hela-S3	cervix
9	chr6:30778600-30782600	Enhancers	Stomach Mucosa	stomach
10	chr6:30778600-30782800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:30778600-30782800	Enhancers	Placenta	Placenta
12	chr6:30778600-30783000	Enhancers	NHEK	skin
13	chr6:30778800-30781200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:30779000-30780600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:30779000-30780600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:30779000-30780600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:30779000-30780600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:30779000-30780800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:30779000-30781000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:30779000-30781000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:30779000-30781000	Weak transcription	A549	lung
22	chr6:30779000-30781800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:30779000-30782000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:30779000-30782000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:30779000-30782800	Enhancers	GM12878-XiMat	blood
26	chr6:30779000-30784800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:30779000-30794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:30779000-30795800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:30779200-30780600	Weak transcription	Right Atrium	heart
30	chr6:30779200-30780800	Weak transcription	Primary B cells from cord blood	blood
31	chr6:30779200-30780800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:30779200-30781000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:30779200-30781200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:30779200-30781600	Weak transcription	Thymus	Thymus
35	chr6:30779200-30782400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr6:30779200-30790000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:30779400-30780600	Weak transcription	Colonic Mucosa	Colon
38	chr6:30779400-30781000	Weak transcription	Esophagus	oesophagus
39	chr6:30779400-30781600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:30779800-30781000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr6:30779800-30781800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:30779800-30782200	Enhancers	HepG2	liver
43	chr6:30779800-30782600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr6:30779800-30783400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr6:30780000-30781000	Weak transcription	HMEC	breast
46	chr6:30780000-30781400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr6:30780000-30783000	Enhancers	HUVEC	blood vessel
48	chr6:30780200-30780600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:30780200-30780600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:30780200-30781000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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