Variant report

Variant	rs2517448
Chromosome Location	chr6:31062667-31062668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30780845..30782405-chr6:31060991..31063180,2	K562	blood:
2	chr6:30701308..30703413-chr6:31060856..31063680,2	MCF-7	breast:
3	chr6:31060052..31062667-chr6:31078284..31080842,2	MCF-7	breast:
4	chr6:31053892..31056272-chr6:31061858..31063779,2	K562	blood:

Variant related genes	Relation type
ENSG00000204542	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2394418	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508014	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517474	0.93[ASN][1000 genomes]
rs2517524	0.86[ASN][1000 genomes]
rs2517527	0.84[ASN][1000 genomes]
rs3130962	0.80[AMR][1000 genomes]
rs3132562	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457327	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6905484	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9263632	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
5	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
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv462746	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv601489	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2517448	HLA-DRB5	cis	multi-tissue	Pritchard
rs2517448	TCF19	Cis_1M	lymphoblastoid	RTeQTL
rs2517448	HLA-C	cis	lymphoblastoid	GTEx
rs2517448	HLA-C///LOC732037	N/A	lymphoblastoid	RTeQTL
rs2517448	PRSS16	cis	cerebellum	SCAN
rs2517448	HCG22	cis	lymphoblastoid	seeQTL
rs2517448	HLA-C	cis	multi-tissue	Pritchard
rs2517448	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs2517448	HCG22	cis	Lymphoblastoid	GTEx
rs2517448	HCG27	Cis_1M	lymphoblastoid	RTeQTL
rs2517448	hmm31752	cis	multi-tissue	Pritchard
rs2517448	HCG27	cis	multi-tissue	Pritchard
rs2517448	HLA-B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31058800-31066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:31059800-31063000	Enhancers	HepG2	liver
3	chr6:31060600-31065200	Enhancers	Primary hematopoietic stem cells	blood
4	chr6:31060800-31062800	Enhancers	A549	lung
5	chr6:31060800-31063200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:31060800-31066800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:31061000-31063000	Enhancers	Brain Substantia Nigra	brain
8	chr6:31061000-31063800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:31061000-31065800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:31061200-31064800	Weak transcription	K562	blood
11	chr6:31061600-31063200	Enhancers	Primary B cells from cord blood	blood
12	chr6:31061600-31063200	Enhancers	Primary B cells from peripheral blood	blood
13	chr6:31061600-31065600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:31061600-31065600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr6:31061800-31062800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:31061800-31062800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:31061800-31063000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr6:31061800-31063000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:31061800-31063200	Enhancers	Brain Anterior Caudate	brain
20	chr6:31061800-31063200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:31061800-31063600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:31061800-31066000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:31062000-31062800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr6:31062000-31062800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr6:31062000-31062800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:31062000-31062800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:31062000-31062800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr6:31062000-31062800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:31062000-31062800	Enhancers	Colonic Mucosa	Colon
30	chr6:31062000-31062800	Enhancers	Fetal Muscle Trunk	muscle
31	chr6:31062000-31062800	Enhancers	Lung	lung
32	chr6:31062000-31062800	Enhancers	Right Atrium	heart
33	chr6:31062000-31063000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:31062000-31063000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:31062000-31063000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr6:31062000-31063000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:31062000-31063000	Enhancers	Brain Cingulate Gyrus	brain
38	chr6:31062000-31063000	Enhancers	Fetal Thymus	thymus
39	chr6:31062000-31063000	Enhancers	Right Ventricle	heart
40	chr6:31062000-31063000	Enhancers	Stomach Mucosa	stomach
41	chr6:31062000-31063000	Enhancers	Thymus	Thymus
42	chr6:31062000-31063000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr6:31062000-31063200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr6:31062000-31063200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr6:31062000-31063200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr6:31062000-31063200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:31062000-31063200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:31062000-31063200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:31062000-31063200	Enhancers	Adipose Nuclei	Adipose
50	chr6:31062000-31063200	Enhancers	Brain Hippocampus Middle	brain

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