Variant report

Variant	rs886424
Chromosome Location	chr6:30782002-30782003
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:32)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30780089..30782522-chr6:30839223..30841388,2	K562	blood:
2	chr6:30583858..30586014-chr6:30781154..30783214,2	K562	blood:
3	chr6:30748021..30750759-chr6:30781042..30784115,3	MCF-7	breast:
4	chr6:30707810..30715390-chr6:30779530..30784762,15	K562	blood:
5	chr6:30744501..30746062-chr6:30781081..30782628,2	K562	blood:
6	chr6:30739130..30742242-chr6:30780166..30782431,3	K562	blood:
7	chr6:30781714..30783791-chr6:30982862..30984438,2	K562	blood:
8	chr6:30766009..30775294-chr6:30775700..30782710,15	MCF-7	breast:
9	chr6:30739945..30741810-chr6:30780568..30783125,2	K562	blood:
10	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
11	chr6:30780643..30783504-chr6:30803282..30805852,2	K562	blood:
12	chr6:30708338..30713459-chr6:30777538..30783709,13	K562	blood:
13	chr6:30522929..30524669-chr6:30781781..30783555,2	K562	blood:
14	chr6:30779954..30784896-chr6:30785156..30789787,6	K562	blood:
15	chr6:30687466..30692169-chr6:30775918..30784078,7	K562	blood:
16	chr6:30780781..30783528-chr6:30792652..30795732,4	K562	blood:
17	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:
18	chr6:30781901..30784193-chr6:30851242..30852873,2	K562	blood:
19	chr6:30780845..30782405-chr6:31060991..31063180,2	K562	blood:
20	chr6:30734312..30736024-chr6:30780945..30783731,2	K562	blood:
21	chr6:30780781..30784942-chr6:30792103..30795715,5	K562	blood:
22	chr6:30760063..30761714-chr6:30779972..30782451,2	K562	blood:
23	chr6:30777633..30780399-chr6:30780437..30782571,2	MCF-7	breast:
24	chr6:30706744..30716171-chr6:30774931..30783832,28	MCF-7	breast:
25	chr6:30760214..30763491-chr6:30779624..30782451,3	K562	blood:
26	chr6:30779859..30782628-chr6:30850009..30853631,3	K562	blood:
27	chr6:30648527..30651008-chr6:30780942..30782992,2	K562	blood:
28	chr6:30655802..30657936-chr6:30780184..30782576,2	K562	blood:
29	chr6:30781732..30783856-chr6:30842291..30844070,2	K562	blood:
30	chr6:30723722..30725318-chr6:30780845..30782479,3	MCF-7	breast:
31	chr6:30720149..30720893-chr6:30781568..30782338,2	MCF-7	breast:
32	chr6:30716968..30722090-chr6:30774929..30783584,12	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IER3-5	chr6:30780643-30782549	ENSG00000214894

No data

Variant related genes	Relation type
ENSG00000204568	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000201988	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000237775	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1049633	0.87[EUR][1000 genomes]
rs1264308	0.87[EUR][1000 genomes]
rs1264325	0.87[EUR][1000 genomes]
rs1264347	0.87[EUR][1000 genomes]
rs1264351	0.95[EUR][1000 genomes]
rs1264361	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264373	0.95[EUR][1000 genomes]
rs2263298	0.89[EUR][1000 genomes]
rs2517578	0.87[EUR][1000 genomes]
rs2524266	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2535328	0.87[EUR][1000 genomes]
rs2535332	0.87[EUR][1000 genomes]
rs2535334	0.87[EUR][1000 genomes]
rs2535340	0.87[EUR][1000 genomes]
rs2844656	0.87[EUR][1000 genomes]
rs2844661	0.86[EUR][1000 genomes]
rs3094088	0.87[EUR][1000 genomes]
rs3094118	0.88[EUR][1000 genomes]
rs3095156	0.84[EUR][1000 genomes]
rs3095326	0.82[EUR][1000 genomes]
rs3095328	0.83[EUR][1000 genomes]
rs3095332	0.83[EUR][1000 genomes]
rs3095334	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129973	0.82[EUR][1000 genomes]
rs3129974	0.83[EUR][1000 genomes]
rs3129977	0.88[EUR][1000 genomes]
rs3129978	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129980	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129981	1.00[ASN][1000 genomes]
rs3129982	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129983	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129984	0.91[EUR][1000 genomes]
rs3129985	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130641	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130665	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130669	1.00[ASN][1000 genomes]
rs3130670	0.85[EUR][1000 genomes]
rs3130673	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131041	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131044	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131045	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131047	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131048	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131049	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131050	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131052	0.94[EUR][1000 genomes]
rs3131054	0.87[EUR][1000 genomes]
rs3131055	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131058	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131060	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131781	0.81[EUR][1000 genomes]
rs3132577	0.87[EUR][1000 genomes]
rs3132599	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132600	0.85[EUR][1000 genomes]
rs3132603	0.89[EUR][1000 genomes]
rs3132605	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45565239	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]
rs56804692	1.00[ASN][1000 genomes]
rs886422	0.87[EUR][1000 genomes]
rs886425	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262200	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262202	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262203	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9262204	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468857	1.00[ASN][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

Variant related diseases (count:1)

Disease	PMID	Source
Bipolar disorder and schizophrenia	22688191	GWAS catalog

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs886424	C6orf1	cis	parietal	SCAN
rs886424	HLA-A	cis	brain	seeQTL
rs886424	HLA-DQA1	cis	multi-tissue	Pritchard
rs886424	HLA-G	cis	multi-tissue	Pritchard
rs886424	HLA-DRB1	cis	multi-tissue	Pritchard
rs886424	HLA-H	cis	multi-tissue	Pritchard
rs886424	HIST1H2BM	cis	cerebellum	SCAN
rs886424	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs886424	HLA-DQB1	cis	multi-tissue	Pritchard
rs886424	BTN3A2	cis	multi-tissue	Pritchard
rs886424	VARSL	cis	multi-tissue	Pritchard
rs886424	ZFP57	cis	multi-tissue	Pritchard
rs886424	HLA-A	cis	multi-tissue	Pritchard
rs886424	HLA-C	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30776400-30783200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr6:30776400-30783400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:30776600-30783400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:30777200-30783200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr6:30778600-30782600	Enhancers	Stomach Mucosa	stomach
6	chr6:30778600-30782800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:30778600-30782800	Enhancers	Placenta	Placenta
8	chr6:30778600-30783000	Enhancers	NHEK	skin
9	chr6:30779000-30782800	Enhancers	GM12878-XiMat	blood
10	chr6:30779000-30784800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:30779000-30794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:30779000-30795800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:30779200-30782400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:30779200-30790000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:30779800-30782200	Enhancers	HepG2	liver
16	chr6:30779800-30782600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:30779800-30783400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:30780000-30783000	Enhancers	HUVEC	blood vessel
19	chr6:30780600-30782200	Enhancers	Colonic Mucosa	Colon
20	chr6:30780600-30782600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:30780600-30782600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:30780600-30782600	Enhancers	Fetal Intestine Small	intestine
23	chr6:30780600-30782600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr6:30780600-30782600	Enhancers	Right Atrium	heart
25	chr6:30780600-30782600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:30780600-30783200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:30780600-30783400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:30780600-30783400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:30780800-30782200	Enhancers	Left Ventricle	heart
30	chr6:30780800-30782400	Enhancers	Primary T cells from cord blood	blood
31	chr6:30780800-30782600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:30780800-30782600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:30780800-30782600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:30780800-30782600	Enhancers	Duodenum Mucosa	Duodenum
35	chr6:30780800-30782600	Enhancers	Fetal Intestine Large	intestine
36	chr6:30780800-30782800	Enhancers	Primary B cells from cord blood	blood
37	chr6:30780800-30782800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:30780800-30782800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr6:30780800-30782800	Enhancers	Osteobl	bone
40	chr6:30780800-30783200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:30780800-30783600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:30781000-30782200	Enhancers	Right Ventricle	heart
43	chr6:30781000-30782600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:30781000-30782600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:30781000-30782600	Enhancers	HSMMtube	muscle
46	chr6:30781000-30782800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:30781000-30782800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr6:30781000-30782800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr6:30781000-30782800	Enhancers	HMEC	breast
50	chr6:30781000-30782800	Enhancers	HSMM	muscle

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