Variant report

Variant	rs6489815
Chromosome Location	chr12:121931211-121931212
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121931071..121932848-chr12:121979141..121982092,2	MCF-7	breast:
2	chr12:121930467..121932395-chr12:121974294..121977005,2	K562	blood:

Variant related genes	Relation type
ENSG00000089094	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11065592	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065593	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065596	0.93[EUR][1000 genomes]
rs11065598	0.85[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11065602	0.93[JPT][hapmap]
rs11065604	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11837997	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57917116	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60437938	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6489814	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489816	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7307400	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309786	0.93[JPT][hapmap]
rs7316418	0.84[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976858	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6489815	GCN1L1	cis	cerebellum	SCAN
rs6489815	NCOR1	trans	cerebellum	SCAN
rs6489815	NOS1	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121906000-121937800	Weak transcription	Aorta	Aorta
2	chr12:121906000-121938000	Weak transcription	Left Ventricle	heart
3	chr12:121906200-121938000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:121906400-121933400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:121906400-121933400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:121906400-121933800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:121906600-121938000	Weak transcription	NHDF-Ad	bronchial
8	chr12:121908800-121931400	Weak transcription	Fetal Lung	lung
9	chr12:121911400-121946400	Weak transcription	Pancreas	Pancrea
10	chr12:121913000-121938000	Weak transcription	Brain Angular Gyrus	brain
11	chr12:121915000-121938000	Weak transcription	Osteobl	bone
12	chr12:121918200-121938000	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:121919000-121937800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:121919800-121938000	Weak transcription	Ovary	ovary
15	chr12:121924600-121946600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:121925200-121936800	Strong transcription	Fetal Stomach	stomach
17	chr12:121925600-121938000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:121925600-121943200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:121926000-121946200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:121926400-121938000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:121926400-121938000	Weak transcription	HSMMtube	muscle
22	chr12:121926600-121932000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:121926600-121936400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:121926800-121934200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:121927200-121932200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:121927400-121933800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:121928400-121933400	Weak transcription	Brain Substantia Nigra	brain
28	chr12:121928400-121934400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:121928400-121938000	Weak transcription	Right Ventricle	heart
30	chr12:121928600-121933400	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:121928600-121934800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:121928600-121937800	Weak transcription	Brain Germinal Matrix	brain
33	chr12:121928600-121937800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:121928600-121938000	Weak transcription	Brain Anterior Caudate	brain
35	chr12:121928600-121941400	Weak transcription	Gastric	stomach
36	chr12:121928600-121945200	Weak transcription	Lung	lung
37	chr12:121928600-121946400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:121928600-121965800	Weak transcription	Hela-S3	cervix
39	chr12:121928800-121933400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:121928800-121937600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:121928800-121937800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:121928800-121937800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:121928800-121938000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:121928800-121938000	Weak transcription	Adipose Nuclei	Adipose
45	chr12:121928800-121938000	Weak transcription	Fetal Heart	heart
46	chr12:121928800-121946000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:121928800-121946400	Weak transcription	NHLF	lung
48	chr12:121929000-121932200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:121929000-121934600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr12:121929000-121934600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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