Variant report

Variant	rs8139950
Chromosome Location	chr22:31037370-31037371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31037150..31040336-chr22:31042164..31045603,3	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1005887	0.86[CHB][hapmap]
rs10439913	0.81[AMR][1000 genomes]
rs1076301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11089468	0.89[ASN][1000 genomes]
rs12159167	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13054505	0.83[EUR][1000 genomes]
rs13056901	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1544468	0.80[EUR][1000 genomes]
rs1801198	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1971653	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1981590	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981591	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072194	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2078976	0.87[ASN][1000 genomes]
rs2240002	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2267163	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs2267164	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs2270013	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3179442	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3887855	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4353747	0.81[EUR][1000 genomes]
rs4375972	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4513384	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4820023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4820891	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5019308	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749141	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749142	0.81[EUR][1000 genomes]
rs5749143	0.81[EUR][1000 genomes]
rs5749144	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5749145	0.81[EUR][1000 genomes]
rs5749147	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5749148	0.82[EUR][1000 genomes]
rs5749149	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5753236	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs5753250	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753252	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs5753257	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs5753259	0.82[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753260	0.83[EUR][1000 genomes]
rs5753265	0.87[ASN][1000 genomes]
rs5994328	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997704	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs5997709	0.80[EUR][1000 genomes]
rs5997710	0.81[EUR][1000 genomes]
rs5997711	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997714	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997715	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713853	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7289553	0.81[EUR][1000 genomes]
rs731990	0.80[EUR][1000 genomes]
rs731991	0.81[EUR][1000 genomes]
rs757027	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs8138932	0.94[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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8139950	CRYBB3	cis	parietal	SCAN
rs8139950	LIF	cis	parietal	SCAN
rs8139950	PES1	cis	parietal	SCAN
rs8139950	DUSP18	cis	lymphoblastoid	seeQTL
rs8139950	MORC2	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31032400-31052400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:31032800-31046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:31033200-31039200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr22:31033200-31052000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:31033400-31058200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr22:31033600-31058000	Weak transcription	Adipose Nuclei	Adipose
7	chr22:31033600-31058000	Weak transcription	Fetal Lung	lung
8	chr22:31033800-31039000	Weak transcription	HSMMtube	muscle
9	chr22:31033800-31039400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:31033800-31039400	Weak transcription	NHLF	lung
11	chr22:31033800-31042600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr22:31033800-31046600	Weak transcription	Fetal Intestine Small	intestine
13	chr22:31033800-31057600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr22:31034000-31039400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr22:31034000-31039400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr22:31034000-31039400	Weak transcription	Fetal Brain Male	brain
17	chr22:31034000-31039400	Weak transcription	Pancreas	Pancrea
18	chr22:31034000-31039400	Weak transcription	Osteobl	bone
19	chr22:31034000-31039600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr22:31034000-31039800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr22:31034000-31039800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr22:31034000-31042200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr22:31034000-31042400	Weak transcription	Brain Germinal Matrix	brain
24	chr22:31034000-31043000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr22:31034000-31045000	Weak transcription	HUVEC	blood vessel
26	chr22:31034000-31045000	Weak transcription	NHEK	skin
27	chr22:31034000-31045200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr22:31034000-31045400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr22:31034000-31046400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr22:31034000-31049800	Weak transcription	Fetal Brain Female	brain
31	chr22:31034000-31059400	Weak transcription	Aorta	Aorta
32	chr22:31034200-31039200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr22:31034200-31039400	Weak transcription	Ovary	ovary
34	chr22:31034200-31045600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr22:31034200-31057800	Weak transcription	Colon Smooth Muscle	Colon
36	chr22:31034200-31058800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr22:31034400-31039400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr22:31036200-31037400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr22:31036200-31038200	Enhancers	Brain Hippocampus Middle	brain
40	chr22:31036200-31041400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr22:31036400-31037400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr22:31036400-31037400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr22:31036400-31037400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr22:31036400-31037400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr22:31036400-31037400	Enhancers	Brain Anterior Caudate	brain
46	chr22:31036400-31037400	Enhancers	Fetal Muscle Trunk	muscle
47	chr22:31036400-31037400	Enhancers	Right Ventricle	heart
48	chr22:31036400-31037400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr22:31036400-31037600	Enhancers	Brain Cingulate Gyrus	brain
50	chr22:31036400-31038000	Enhancers	Right Atrium	heart

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