Variant report

Variant	rs5763378
Chromosome Location	chr22:30034994-30034995
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11090572	0.91[EUR][1000 genomes]
rs11704455	0.81[EUR][1000 genomes]
rs12165952	0.94[EUR][1000 genomes]
rs13054076	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800539	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2007668	0.93[JPT][hapmap]
rs2079647	0.93[JPT][hapmap]
rs2158619	0.86[CEU][hapmap]
rs2245194	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2283860	0.93[JPT][hapmap]
rs2348686	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2527334	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2527335	0.87[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2530661	0.93[JPT][hapmap]
rs2530662	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531844	0.93[JPT][hapmap]
rs2857638	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2857643	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2857646	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2857647	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2857652	0.86[CEU][hapmap]
rs456300	0.93[JPT][hapmap]
rs465938	0.93[JPT][hapmap]
rs467812	0.93[JPT][hapmap]
rs468217	0.93[JPT][hapmap]
rs468902	0.93[JPT][hapmap]
rs4823049	0.90[EUR][1000 genomes]
rs55684603	0.82[EUR][1000 genomes]
rs56246484	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5752946	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5763296	0.93[JPT][hapmap]
rs5763302	0.93[JPT][hapmap]
rs5763304	0.93[JPT][hapmap]
rs5763354	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6006179	0.93[JPT][hapmap]
rs62227968	0.89[EUR][1000 genomes]
rs6361	0.93[JPT][hapmap]
rs6519793	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs7290811	0.81[AMR][1000 genomes]
rs731647	0.90[CEU][hapmap]
rs737976	0.93[JPT][hapmap]
rs737977	0.93[JPT][hapmap]
rs756053	0.86[CEU][hapmap]
rs8140060	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs9613968	0.93[JPT][hapmap]
rs9613976	0.93[JPT][hapmap]
rs9625841	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs5763378	PITPNB	cis	cerebellum	SCAN
rs5763378	NIPSNAP1	cis	parietal	SCAN
rs5763378	C11orf1	trans	parietal	SCAN
rs5763378	KIAA1671	cis	cerebellum	SCAN
rs5763378	CRYBB3	cis	parietal	SCAN
rs5763378	THOC5	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
4	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
5	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
6	chr22:30021800-30041600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr22:30022000-30037200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr22:30022000-30038400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr22:30022200-30053400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr22:30023000-30037400	Weak transcription	Hela-S3	cervix
11	chr22:30023200-30038600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr22:30023600-30037800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr22:30023800-30038200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr22:30023800-30038600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr22:30024000-30037400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr22:30024200-30038200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr22:30026400-30038000	Weak transcription	Brain Angular Gyrus	brain
18	chr22:30026800-30035200	Weak transcription	Fetal Stomach	stomach
19	chr22:30026800-30038200	Weak transcription	Spleen	Spleen
20	chr22:30026800-30055800	Weak transcription	Gastric	stomach
21	chr22:30027200-30044400	Weak transcription	Brain Substantia Nigra	brain
22	chr22:30027400-30038000	Weak transcription	Colon Smooth Muscle	Colon
23	chr22:30027600-30038200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr22:30027600-30057200	Weak transcription	Brain Hippocampus Middle	brain
25	chr22:30027800-30056000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr22:30028400-30037600	Weak transcription	Fetal Intestine Large	intestine
27	chr22:30028400-30044400	Weak transcription	Pancreas	Pancrea
28	chr22:30028800-30037400	Weak transcription	HepG2	liver
29	chr22:30029600-30035000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr22:30029600-30053800	Weak transcription	Esophagus	oesophagus
31	chr22:30030000-30038400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr22:30030200-30036400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr22:30030400-30037200	Weak transcription	NHDF-Ad	bronchial
34	chr22:30030400-30038000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr22:30031200-30035000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr22:30031200-30037600	Weak transcription	A549	lung
37	chr22:30032200-30035000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr22:30032200-30047000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr22:30032200-30057000	Weak transcription	Colonic Mucosa	Colon
40	chr22:30032200-30070000	Weak transcription	Fetal Brain Male	brain
41	chr22:30032400-30039200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr22:30032400-30039400	Strong transcription	Primary T cells from cord blood	blood
43	chr22:30032600-30036600	Strong transcription	Fetal Thymus	thymus
44	chr22:30032600-30036600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr22:30032600-30036800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr22:30032600-30036800	Strong transcription	Dnd41	blood
47	chr22:30032600-30039200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr22:30032800-30035200	Strong transcription	Primary B cells from cord blood	blood
49	chr22:30032800-30035400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr22:30032800-30035400	Strong transcription	Thymus	Thymus

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