Variant report

Variant	rs589428
Chromosome Location	chr6:31848220-31848221
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31847754-31848295	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31845609..31848674-chr6:31849036..31853301,8	K562	blood:
2	chr6:31847413..31850386-chr6:31864016..31867954,3	MCF-7	breast:
3	chr6:31802504..31804188-chr6:31847316..31849338,2	MCF-7	breast:
4	chr6:31846387..31850562-chr6:31859687..31861704,3	MCF-7	breast:
5	chr6:31632488..31634160-chr6:31845506..31848503,2	MCF-7	breast:
6	chr6:31631416..31634262-chr6:31846927..31849993,4	K562	blood:
7	chr6:31847746..31849844-chr6:31938872..31940807,2	MCF-7	breast:
8	chr6:31846978..31851415-chr6:31853585..31859166,6	K562	blood:
9	chr6:31847963..31849959-chr6:31859200..31861455,2	K562	blood:

No data

Variant related genes	Relation type
SLC44A4	TF binding region
EHMT2-AS1	TF binding region
ENSG00000237080	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000201823	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204344	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204348	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000263020	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2227956	0.80[ASN][1000 genomes]
rs2763981	0.92[ASN][1000 genomes]
rs486416	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs521977	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs535586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659445	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7451017	0.92[ASN][1000 genomes]
rs9267577	0.90[ASN][1000 genomes]
rs9267649	0.92[ASN][1000 genomes]
rs9267659	0.98[ASN][1000 genomes]
rs9394078	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
2	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
3	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	378 gene(s)	inside rSNPs	diseases
5	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
7	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
9	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
10	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
11	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer 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	257 gene(s)	inside rSNPs	diseases
12	nsv884428	chr6:31728102-31870326	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
13	nsv462872	chr6:31778272-31864304	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
14	nsv601945	chr6:31778272-31864304	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
15	nsv601950	chr6:31785438-32492308	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
16	nsv601951	chr6:31785438-32496748	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' 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	197 gene(s)	inside rSNPs	diseases
17	nsv601955	chr6:31785453-32484368	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
18	nsv601956	chr6:31785453-32492308	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
19	nsv462874	chr6:31794592-31864304	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
20	nsv601959	chr6:31794592-31864304	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
21	nsv884472	chr6:31813898-31870856	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
22	nsv508399	chr6:31829474-31902423	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
23	nsv884474	chr6:31836055-31870326	Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
24	nsv462875	chr6:31838441-31907147	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
25	nsv601960	chr6:31838441-31907147	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
26	nsv884475	chr6:31840625-31880320	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
27	nsv884476	chr6:31848000-31870326	Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs589428	HLA-DQB1	cis	lymphoblastoid	seeQTL
rs589428	HLA-C	cis	Whole Blood	GTEx
rs589428	HLA-DQA1	cis	lymphoblastoid	seeQTL
rs589428	HLA-C	cis	Artery Tibial	GTEx
rs589428	HLA-C	cis	lymphoblastoid	GTEx
rs589428	XXbac-BPG248L24.12	cis	Whole Blood	GTEx
rs589428	HLA-DRB1	cis	lymphoblastoid	seeQTL
rs589428	HLA-DRB5	cis	lymphoblastoid	GTEx
rs589428	HMGA1	cis	cerebellum	SCAN
rs589428	HLA-DRB5	cis	lymphoblastoid	seeQTL
rs589428	HLA-DRB5	cis	cerebellum	SCAN
rs589428	LOC222699	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31832000-31856000	Weak transcription	Right Atrium	heart
2	chr6:31832400-31850800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr6:31833200-31864200	Weak transcription	Fetal Heart	heart
4	chr6:31839000-31849000	Weak transcription	HSMM	muscle
5	chr6:31839200-31848800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:31842800-31848800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:31843000-31848800	Weak transcription	K562	blood
8	chr6:31845000-31848800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:31845400-31848600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:31845600-31849200	Weak transcription	HUVEC	blood vessel
11	chr6:31846200-31850000	Weak transcription	Psoas Muscle	Psoas
12	chr6:31846400-31849000	Weak transcription	Fetal Brain Male	brain
13	chr6:31846800-31849000	Weak transcription	Fetal Kidney	kidney
14	chr6:31847000-31850200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:31847000-31857800	Strong transcription	Osteobl	bone
16	chr6:31847000-31860800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:31847000-31863200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:31847000-31863600	Strong transcription	Fetal Brain Female	brain
19	chr6:31847000-31864000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:31847200-31848400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:31847200-31849200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:31847200-31850200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:31847200-31857600	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr6:31847200-31860600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:31847200-31861400	Strong transcription	Spleen	Spleen
26	chr6:31847200-31863800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:31847200-31864000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:31847200-31864200	Strong transcription	Fetal Stomach	stomach
29	chr6:31847200-31864200	Strong transcription	Thymus	Thymus
30	chr6:31847400-31848600	Strong transcription	GM12878-XiMat	blood
31	chr6:31847400-31848800	Enhancers	HSMMtube	muscle
32	chr6:31847400-31850000	Strong transcription	Brain Hippocampus Middle	brain
33	chr6:31847400-31850200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr6:31847400-31850200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:31847400-31850200	Strong transcription	NHLF	lung
36	chr6:31847400-31850400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr6:31847400-31851000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:31847400-31852600	Strong transcription	Pancreas	Pancrea
39	chr6:31847400-31852800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:31847400-31853000	Strong transcription	Brain Angular Gyrus	brain
41	chr6:31847400-31853200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:31847400-31853200	Strong transcription	Left Ventricle	heart
43	chr6:31847400-31853600	Strong transcription	Colon Smooth Muscle	Colon
44	chr6:31847400-31856200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:31847400-31857400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr6:31847400-31857600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:31847400-31857600	Strong transcription	Right Ventricle	heart
48	chr6:31847400-31858000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:31847400-31858000	Strong transcription	Lung	lung
50	chr6:31847400-31858200	Strong transcription	H9 Cell Line	embryonic stem cell

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