Variant report

Variant	rs7582382
Chromosome Location	chr2:99386960-99386961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99344922..99348721-chr2:99382903..99389092,6	MCF-7	breast:
2	chr2:99385437..99388262-chr2:99414976..99417069,2	MCF-7	breast:
3	chr2:99345368..99349321-chr2:99385005..99390572,6	MCF-7	breast:
4	chr2:99384896..99387607-chr2:99394803..99397192,2	MCF-7	breast:
5	chr2:99386151..99388080-chr2:99407312..99410170,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10166044	0.82[ASN][1000 genomes]
rs10189330	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615689	0.89[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs12999225	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13000014	0.81[CEU][hapmap]
rs13389386	0.91[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs1356424	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2276604	0.82[CHB][hapmap]
rs6712597	0.83[ASN][1000 genomes]
rs6716514	0.83[ASN][1000 genomes]
rs6757099	0.81[ASN][1000 genomes]
rs7557295	0.85[ASN][1000 genomes]
rs7561818	0.82[CEU][hapmap]
rs7570815	0.85[ASN][1000 genomes]
rs7573844	0.82[CEU][hapmap]
rs7578035	0.89[EUR][1000 genomes]
rs7581128	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7581349	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs9308815	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7582382	ARID5A	cis	parietal	SCAN
rs7582382	FAHD2B	cis	parietal	SCAN
rs7582382	INPP4A	cis	cerebellum	SCAN
rs7582382	MAP4K4	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99373800-99388000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:99378400-99389400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:99378800-99388200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:99379200-99388200	Weak transcription	Brain Substantia Nigra	brain
5	chr2:99379400-99388400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:99380600-99387400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:99380600-99387400	Weak transcription	Adipose Nuclei	Adipose
8	chr2:99383800-99387000	Enhancers	HUVEC	blood vessel
9	chr2:99384400-99389800	Flanking Active TSS	Dnd41	blood
10	chr2:99384800-99388400	Enhancers	Placenta	Placenta
11	chr2:99385000-99388000	Enhancers	Pancreas	Pancrea
12	chr2:99385000-99389400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr2:99385200-99388200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:99385400-99387000	Enhancers	Primary hematopoietic stem cells	blood
15	chr2:99385400-99388200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:99385600-99387400	Weak transcription	Spleen	Spleen
17	chr2:99385800-99387600	Weak transcription	Liver	Liver
18	chr2:99385800-99387600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:99385800-99388200	Weak transcription	HMEC	breast
20	chr2:99385800-99394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:99385800-99410400	Weak transcription	Right Atrium	heart
22	chr2:99386000-99387800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:99386000-99388400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:99386200-99387000	Enhancers	Small Intestine	intestine
25	chr2:99386200-99389000	Flanking Active TSS	Fetal Thymus	thymus
26	chr2:99386200-99389200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr2:99386200-99391600	Weak transcription	Fetal Brain Female	brain
28	chr2:99386400-99387000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:99386400-99387000	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr2:99386400-99388000	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:99386400-99389000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr2:99386600-99387000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:99386600-99387000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr2:99386600-99387000	Active TSS	HSMM	muscle
35	chr2:99386600-99387400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr2:99386600-99387400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:99386600-99387600	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr2:99386600-99387600	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr2:99386600-99387800	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr2:99386600-99388200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:99386600-99388200	Weak transcription	Lung	lung
42	chr2:99386600-99391000	Weak transcription	Fetal Brain Male	brain
43	chr2:99386800-99387000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:99386800-99387000	Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr2:99386800-99387000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:99386800-99387200	Weak transcription	GM12878-XiMat	blood
47	chr2:99386800-99387400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:99386800-99387400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr2:99386800-99387400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:99386800-99387400	Active TSS	Thymus	Thymus

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