Variant report

Variant	rs4669775
Chromosome Location	chr2:11850369-11850370
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	chr2:11837517..11840283-chr2:11849750..11852700,2	MCF-7	breast:
2	chr2:11832559..11835214-chr2:11848775..11850407,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10180912	0.81[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs10929769	0.80[AMR][1000 genomes]
rs12052681	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12465629	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12465630	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12692445	0.80[AMR][1000 genomes]
rs13036247	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4389306	0.83[EUR][1000 genomes]
rs4542816	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4668739	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669772	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4669774	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62116211	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6432230	0.86[CEU][hapmap]
rs6432231	0.85[CEU][hapmap]
rs6736021	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7597788	0.84[EUR][1000 genomes]
rs7598716	0.82[EUR][1000 genomes]

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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS 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 miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv469449	chr2:11808654-11854012	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv580972	chr2:11808654-11854012	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4669775	NBAS	cis	cerebellum	SCAN
rs4669775	LPIN1	cis	parietal	SCAN
rs4669775	LPIN1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11844200-11854200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:11844600-11856400	Weak transcription	Psoas Muscle	Psoas
3	chr2:11845800-11851000	Weak transcription	Liver	Liver
4	chr2:11848200-11851000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:11848600-11852200	Weak transcription	Placenta	Placenta
6	chr2:11848800-11854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:11848800-11855400	Weak transcription	Pancreas	Pancrea
8	chr2:11849000-11854400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:11849400-11852800	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:11849800-11851200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:11849800-11851400	Enhancers	HMEC	breast
12	chr2:11849800-11851400	Enhancers	NH-A	brain
13	chr2:11849800-11852000	Enhancers	Colon Smooth Muscle	Colon
14	chr2:11849800-11852800	Enhancers	NHLF	lung
15	chr2:11849800-11853200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:11849800-11853200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:11849800-11853400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:11850000-11850600	Enhancers	Adipose Nuclei	Adipose
19	chr2:11850000-11850600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:11850000-11850800	Enhancers	Aorta	Aorta
21	chr2:11850000-11850800	Enhancers	HUVEC	blood vessel
22	chr2:11850000-11851000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:11850000-11851400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:11850000-11851400	Enhancers	Rectal Smooth Muscle	rectum
25	chr2:11850000-11851400	Enhancers	NHEK	skin
26	chr2:11850000-11851600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:11850000-11851600	Enhancers	NHDF-Ad	bronchial
28	chr2:11850000-11851600	Enhancers	Osteobl	bone
29	chr2:11850000-11852000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:11850000-11852000	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:11850000-11852600	Enhancers	Brain Substantia Nigra	brain
32	chr2:11850000-11852600	Enhancers	Ovary	ovary
33	chr2:11850200-11850400	Enhancers	Fetal Brain Male	brain
34	chr2:11850200-11850800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:11850200-11851000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr2:11850200-11851000	Enhancers	A549	lung
37	chr2:11850200-11851400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:11850200-11851400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:11850200-11851400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:11850200-11851800	Enhancers	Fetal Lung	lung
41	chr2:11850200-11851800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:11850200-11852000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:11850200-11852000	Enhancers	Fetal Stomach	stomach
44	chr2:11850200-11852600	Enhancers	Brain Hippocampus Middle	brain
45	chr2:11850200-11852800	Enhancers	Brain Angular Gyrus	brain

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