Variant report

Variant	rs3824908
Chromosome Location	chr11:76077320-76077321
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:76075524..76077894-chr11:76154235..76156946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158636	Chromatin interaction
ENSG00000255135	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11236718	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2226895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2618063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2618064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2618092	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2851154	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851473	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851475	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851477	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv521451	chr11:76053527-76087844	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3439808	chr11:76074633-76079115	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3824908	PDE2A	cis	cerebellum	SCAN
rs3824908	DNAJB13	cis	parietal	SCAN
rs3824908	SNORD15B	cis	cerebellum	SCAN
rs3824908	B3GNT6	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76054600-76080600	Weak transcription	Psoas Muscle	Psoas
2	chr11:76056800-76080600	Weak transcription	Small Intestine	intestine
3	chr11:76059000-76082000	Weak transcription	HMEC	breast
4	chr11:76062600-76079200	Weak transcription	Stomach Mucosa	stomach
5	chr11:76066000-76077600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:76066200-76079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:76066200-76085800	Weak transcription	Esophagus	oesophagus
8	chr11:76066400-76079600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:76066400-76089200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:76066400-76090000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:76066600-76080600	Weak transcription	Spleen	Spleen
12	chr11:76066600-76082000	Weak transcription	Right Ventricle	heart
13	chr11:76066600-76082000	Weak transcription	NH-A	brain
14	chr11:76066600-76090000	Weak transcription	Fetal Brain Female	brain
15	chr11:76066800-76082000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:76067400-76077800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:76067400-76080600	Weak transcription	Right Atrium	heart
18	chr11:76067400-76082000	Weak transcription	NHLF	lung
19	chr11:76067600-76079000	Weak transcription	Fetal Lung	lung
20	chr11:76067600-76079400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:76067600-76082000	Weak transcription	Aorta	Aorta
22	chr11:76067600-76082000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:76067600-76082000	Weak transcription	GM12878-XiMat	blood
24	chr11:76067600-76082000	Weak transcription	NHEK	skin
25	chr11:76067600-76082200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:76067600-76082400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:76067600-76085800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:76067600-76090400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:76067600-76091000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:76067800-76079200	Weak transcription	Fetal Kidney	kidney
31	chr11:76067800-76079400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr11:76067800-76080400	Weak transcription	Liver	Liver
33	chr11:76067800-76080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:76067800-76082200	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:76067800-76087400	Weak transcription	Colonic Mucosa	Colon
36	chr11:76067800-76090000	Weak transcription	Lung	lung
37	chr11:76068200-76080400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:76068200-76082000	Weak transcription	HUVEC	blood vessel
39	chr11:76068400-76077800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:76068400-76080000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:76068400-76080600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:76070600-76077400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr11:76071200-76082000	Weak transcription	A549	lung
44	chr11:76071400-76079200	Weak transcription	Fetal Intestine Large	intestine
45	chr11:76071400-76082200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:76071800-76077400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr11:76071800-76078400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:76071800-76078800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr11:76071800-76080600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:76071800-76082200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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