Variant report

Variant	rs3852585
Chromosome Location	chr12:120513625-120513626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120504846..120507314-chr12:120512552..120515241,2	MCF-7	breast:
2	chr12:120513025..120515032-chr12:120727834..120729863,2	MCF-7	breast:
3	chr12:120513305..120516227-chr12:120637401..120638998,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089157	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10732609	1.00[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10774539	0.93[EUR][1000 genomes]
rs10774540	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852587	1.00[CEU][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3936255	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5028648	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961547	0.85[EUR][1000 genomes]
rs7974498	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3852585	GCN1L1	cis	parietal	SCAN
rs3852585	SRSF9	cis	parietal	SCAN
rs3852585	WSB2	cis	parietal	SCAN
rs3852585	GCN1L1	cis	multi-tissue	Pritchard
rs3852585	OASL	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120493800-120523800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:120494800-120517800	Weak transcription	Lung	lung
3	chr12:120498800-120516600	Weak transcription	Fetal Brain Male	brain
4	chr12:120499800-120516400	Weak transcription	Primary B cells from cord blood	blood
5	chr12:120502000-120523400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:120502200-120516600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:120502200-120517800	Weak transcription	Gastric	stomach
8	chr12:120502400-120523200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:120502400-120523400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:120502400-120524400	Weak transcription	Fetal Intestine Small	intestine
11	chr12:120502600-120518400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:120502600-120524400	Weak transcription	Brain Anterior Caudate	brain
13	chr12:120502600-120525200	Weak transcription	Spleen	Spleen
14	chr12:120502800-120514200	Weak transcription	Hela-S3	cervix
15	chr12:120503000-120517000	Weak transcription	Dnd41	blood
16	chr12:120503600-120516000	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:120503800-120518000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:120504600-120516800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:120504600-120516800	Weak transcription	HMEC	breast
20	chr12:120505800-120516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:120507400-120514600	Weak transcription	Stomach Mucosa	stomach
22	chr12:120507400-120516800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:120508400-120518200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:120509800-120514600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:120509800-120524600	Weak transcription	Pancreas	Pancrea
26	chr12:120510000-120514800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:120510000-120524600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:120510200-120523000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:120510400-120517600	Weak transcription	Fetal Brain Female	brain
30	chr12:120510400-120517800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:120510600-120514400	Weak transcription	Esophagus	oesophagus
32	chr12:120510600-120524600	Weak transcription	Brain Germinal Matrix	brain
33	chr12:120511000-120514400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:120511000-120516600	Weak transcription	NHEK	skin
35	chr12:120511200-120516600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:120511600-120523200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:120512000-120513800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:120512600-120514400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:120512800-120514200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:120512800-120524400	Weak transcription	Brain Angular Gyrus	brain
41	chr12:120513200-120514400	Weak transcription	Fetal Thymus	thymus
42	chr12:120513200-120514600	Weak transcription	Placenta	Placenta
43	chr12:120513200-120516000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:120513200-120516200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:120513200-120516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:120513200-120517800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:120513400-120514600	Weak transcription	Thymus	Thymus
48	chr12:120513400-120515200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:120513400-120516000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:120513400-120516800	Weak transcription	Primary B cells from peripheral blood	blood

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