Variant report

Variant	rs1122239
Chromosome Location	chr22:30437658-30437659
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12233358	0.92[ASN][1000 genomes]
rs12483946	0.85[CHB][hapmap]
rs12484547	0.83[ASN][1000 genomes]
rs12484983	0.81[CHB][hapmap]
rs13053765	0.86[ASN][1000 genomes]
rs13054837	0.83[ASN][1000 genomes]
rs13056332	0.83[ASN][1000 genomes]
rs13057204	0.92[ASN][1000 genomes]
rs13057580	0.83[ASN][1000 genomes]
rs13057733	0.89[ASN][1000 genomes]
rs13057878	0.83[ASN][1000 genomes]
rs1476514	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2010916	0.98[ASN][1000 genomes]
rs2012308	0.92[ASN][1000 genomes]
rs2214047	0.83[ASN][1000 genomes]
rs2412977	0.83[ASN][1000 genomes]
rs2412979	0.83[ASN][1000 genomes]
rs34474867	0.83[ASN][1000 genomes]
rs34545612	0.83[ASN][1000 genomes]
rs35067150	0.82[ASN][1000 genomes]
rs35710453	0.89[ASN][1000 genomes]
rs36018230	0.89[ASN][1000 genomes]
rs4820829	0.83[ASN][1000 genomes]
rs4823067	0.92[ASN][1000 genomes]
rs4823071	0.86[ASN][1000 genomes]
rs4823080	0.85[CHB][hapmap]
rs5753002	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5753007	0.87[ASN][1000 genomes]
rs5753013	0.83[ASN][1000 genomes]
rs5753014	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs5753015	0.83[ASN][1000 genomes]
rs5753019	0.83[ASN][1000 genomes]
rs5753020	0.83[ASN][1000 genomes]
rs5753022	0.83[ASN][1000 genomes]
rs5753028	0.83[ASN][1000 genomes]
rs5753029	0.83[ASN][1000 genomes]
rs5753030	0.83[ASN][1000 genomes]
rs5763734	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5763742	0.92[ASN][1000 genomes]
rs5763746	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5763748	0.92[ASN][1000 genomes]
rs5763749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763750	0.89[ASN][1000 genomes]
rs5763758	0.86[ASN][1000 genomes]
rs5763763	0.86[ASN][1000 genomes]
rs5763766	0.86[ASN][1000 genomes]
rs5763769	0.86[ASN][1000 genomes]
rs5763774	0.86[ASN][1000 genomes]
rs5763782	0.86[ASN][1000 genomes]
rs5763787	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5763788	0.83[ASN][1000 genomes]
rs5763805	0.83[ASN][1000 genomes]
rs5763810	0.83[ASN][1000 genomes]
rs5763825	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763852	0.83[ASN][1000 genomes]
rs5763854	0.83[ASN][1000 genomes]
rs5763861	0.83[ASN][1000 genomes]
rs5763872	0.85[CHB][hapmap]
rs6006393	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs6006399	0.89[EUR][1000 genomes]
rs718773	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7286304	0.87[ASN][1000 genomes]
rs7286681	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs739616	0.89[ASN][1000 genomes]
rs757026	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs766011	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs975704	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[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	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
rs1122239	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 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	chr22:30435000-30437800	Weak transcription	NHEK	skin
21	chr22:30435000-30438000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr22:30435000-30438600	Weak transcription	NHDF-Ad	bronchial
23	chr22:30435000-30438800	Weak transcription	Hela-S3	cervix
24	chr22:30435000-30438800	Weak transcription	HUVEC	blood vessel
25	chr22:30435000-30439200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr22:30435000-30439400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr22:30435000-30439600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr22:30435000-30439600	Weak transcription	Adipose Nuclei	Adipose
29	chr22:30435000-30439600	Weak transcription	Stomach Mucosa	stomach
30	chr22:30435000-30439600	Weak transcription	HMEC	breast
31	chr22:30435000-30439600	Weak transcription	NH-A	brain
32	chr22:30435000-30439600	Weak transcription	NHLF	lung
33	chr22:30435000-30439800	Weak transcription	Pancreas	Pancrea
34	chr22:30435000-30439800	Weak transcription	HSMM	muscle
35	chr22:30435000-30439800	Weak transcription	Osteobl	bone
36	chr22:30435000-30440000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:30435000-30440000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr22:30435000-30440200	Weak transcription	A549	lung
39	chr22:30435000-30440400	Weak transcription	Liver	Liver
40	chr22:30435000-30440600	Weak transcription	Lung	lung
41	chr22:30435000-30450600	Weak transcription	Gastric	stomach
42	chr22:30436600-30437800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr22:30436600-30439800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr22:30436800-30440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr22:30437000-30438000	Weak transcription	Placenta	Placenta
46	chr22:30437000-30438600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:30437000-30443400	Weak transcription	Esophagus	oesophagus
48	chr22:30437600-30438200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr22:30437600-30438200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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