Variant report

Variant	rs41177
Chromosome Location	chr22:30438447-30438448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30438208..30440185-chr22:30440933..30443498,2	MCF-7	breast:
2	chr22:30431981..30436228-chr22:30436988..30442132,5	MCF-7	breast:
3	chr22:30436980..30439032-chr22:30450263..30452831,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227201	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12537	0.96[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1468177	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2412974	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41162	0.80[CEU][hapmap]
rs41172	0.92[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs41174	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs41178	0.88[EUR][1000 genomes]
rs5763793	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6006356	0.81[YRI][hapmap]
rs718772	0.80[CEU][hapmap]
rs8141404	0.80[CEU][hapmap]
rs9625919	0.80[CEU][hapmap]
rs9625921	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41177	OSBP2	cis	temporal cortex	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30423600-30447600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:30424800-30443000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr22:30425200-30438800	Weak transcription	Fetal Intestine Large	intestine
4	chr22:30425200-30440000	Weak transcription	Fetal Lung	lung
5	chr22:30425200-30440200	Weak transcription	Brain Germinal Matrix	brain
6	chr22:30425600-30439400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr22:30425800-30439800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr22:30425800-30442000	Weak transcription	Fetal Brain Female	brain
9	chr22:30426600-30443000	Weak transcription	Thymus	Thymus
10	chr22:30429400-30439800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr22:30430200-30442800	Weak transcription	Spleen	Spleen
12	chr22:30430200-30449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr22:30430800-30439400	Weak transcription	Fetal Intestine Small	intestine
14	chr22:30432800-30438800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr22:30432800-30439600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr22:30432800-30439800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr22:30432800-30440800	Weak transcription	Fetal Stomach	stomach
18	chr22:30434600-30439800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr22:30434600-30439800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr22:30435000-30438600	Weak transcription	NHDF-Ad	bronchial
21	chr22:30435000-30438800	Weak transcription	Hela-S3	cervix
22	chr22:30435000-30438800	Weak transcription	HUVEC	blood vessel
23	chr22:30435000-30439200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr22:30435000-30439400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr22:30435000-30439600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr22:30435000-30439600	Weak transcription	Adipose Nuclei	Adipose
27	chr22:30435000-30439600	Weak transcription	Stomach Mucosa	stomach
28	chr22:30435000-30439600	Weak transcription	HMEC	breast
29	chr22:30435000-30439600	Weak transcription	NH-A	brain
30	chr22:30435000-30439600	Weak transcription	NHLF	lung
31	chr22:30435000-30439800	Weak transcription	Pancreas	Pancrea
32	chr22:30435000-30439800	Weak transcription	HSMM	muscle
33	chr22:30435000-30439800	Weak transcription	Osteobl	bone
34	chr22:30435000-30440000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr22:30435000-30440000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr22:30435000-30440200	Weak transcription	A549	lung
37	chr22:30435000-30440400	Weak transcription	Liver	Liver
38	chr22:30435000-30440600	Weak transcription	Lung	lung
39	chr22:30435000-30450600	Weak transcription	Gastric	stomach
40	chr22:30436600-30439800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr22:30436800-30440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr22:30437000-30438600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr22:30437000-30443400	Weak transcription	Esophagus	oesophagus
44	chr22:30437800-30438600	Enhancers	NHEK	skin
45	chr22:30438000-30440400	Enhancers	Fetal Kidney	kidney
46	chr22:30438200-30438600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr22:30438200-30439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr22:30438200-30439800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr22:30438200-30448200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr22:30438400-30439600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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