Variant report

Variant	rs2476601
Chromosome Location	chr1:114377568-114377569
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114352576..114359844-chr1:114370702..114381098,32	MCF-7	breast:
2	chr1:114377132..114380200-chr1:114444607..114447875,4	MCF-7	breast:
3	chr1:114376437..114378781-chr1:114506085..114507975,2	MCF-7	breast:
4	chr1:114344419..114346112-chr1:114376286..114378764,3	MCF-7	breast:
5	chr1:114375425..114378067-chr1:114378489..114380651,2	K562	blood:
6	chr1:114371649..114374466-chr1:114376496..114379359,3	K562	blood:
7	chr1:114376626..114379778-chr1:114446255..114449458,6	K562	blood:
8	chr1:114377082..114381758-chr1:114445444..114449368,6	MCF-7	breast:
9	chr1:114366150..114373270-chr1:114373613..114381825,12	MCF-7	breast:
10	chr1:114377224..114379713-chr1:114440605..114443042,2	K562	blood:
11	chr1:114353356..114357634-chr1:114372814..114380576,14	MCF-7	breast:
12	chr1:114372966..114375682-chr1:114376840..114378466,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000118655	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000231128	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1217384	1.00[LWK][hapmap]
rs12760457	1.00[LWK][hapmap]
rs2040040	1.00[LWK][hapmap]
rs3789609	1.00[LWK][hapmap]
rs6674848	1.00[LWK][hapmap]
rs6679677	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6703387	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription 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 target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

Variant related diseases (count:14)

Disease	PMID	Source
Rheumatoid arthritis	24449572	GWAS catalog
Type 1 diabetes	17632545	GWAS catalog
Crohn's disease	18587394	GWAS catalog
Rheumatoid arthritis	17804836	GWAS catalog
Rheumatoid arthritis	19503088	GWAS catalog
Rheumatoid arthritis	24390342	GWAS catalog
Type 1 diabetes autoantibodies	21829393	GWAS catalog
Rheumatoid arthritis	20453842	GWAS catalog
Vitiligo	20410501	GWAS catalog
Crohn's disease	21102463	GWAS catalog
Type 1 diabetes	19430480	GWAS catalog
Rheumatoid arthritis	21156761	GWAS catalog
Myasthenia gravis	23055271	GWAS catalog
Type 1 diabetes	17554260	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2476601	MAGI3	cis	parietal	SCAN
rs2476601	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114355000-114401000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:114355000-114401000	Weak transcription	Spleen	Spleen
3	chr1:114355800-114397400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:114357000-114392200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:114357200-114377600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:114357200-114377800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:114358400-114377600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:114358600-114377600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:114361800-114390400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:114365400-114377600	Strong transcription	GM12878-XiMat	blood
12	chr1:114366800-114379600	Weak transcription	Primary T cells from cord blood	blood
13	chr1:114369000-114380000	Weak transcription	Thymus	Thymus
14	chr1:114370000-114377600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:114375200-114377600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:114375200-114377600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:114375200-114377600	Strong transcription	Fetal Thymus	thymus
18	chr1:114375600-114377600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:114375800-114377600	Strong transcription	Primary B cells from cord blood	blood
20	chr1:114376200-114377600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:114376200-114377600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:114376200-114377600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:114376600-114377600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:114376600-114377600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:114376800-114377600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr1:114376800-114377600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:114376800-114377600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:114376800-114377600	Enhancers	NHEK	skin
29	chr1:114376800-114378000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:114377000-114377600	Enhancers	HMEC	breast
31	chr1:114377200-114377600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:114377400-114377600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
33	chr1:114377400-114377600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:114377400-114377600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:114377400-114377600	Genic enhancers	Dnd41	blood
36	chr1:114377400-114380200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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