Variant report

Variant	rs2857645
Chromosome Location	chr22:30061953-30061954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1034880	0.88[YRI][hapmap];0.91[AFR][1000 genomes]
rs1476757	0.88[YRI][hapmap];0.93[AFR][1000 genomes]
rs2071622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245185	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245415	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252472	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252587	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267150	0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2267151	1.00[ASW][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2283863	0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2283864	0.91[AFR][1000 genomes]
rs2527337	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2530667	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2530668	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2530669	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2530670	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2530672	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2530673	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530675	0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2530676	0.81[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2531850	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857637	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857639	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857640	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857641	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857642	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857648	0.84[CHD][hapmap];0.94[GIH][hapmap];0.84[ASN][1000 genomes]
rs2857650	0.88[YRI][hapmap];0.93[AFR][1000 genomes]
rs2857651	1.00[ASW][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs5752953	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs5763409	0.93[AFR][1000 genomes]
rs5763422	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs5763431	0.90[AFR][1000 genomes]
rs7291645	0.89[CHD][hapmap];0.90[GIH][hapmap]
rs737931	0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9608806	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv529737	chr22:30060946-30109561	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2857645	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs2857645	XBP1	cis	cerebellum	SCAN
rs2857645	PITPNB	cis	cerebellum	SCAN
rs2857645	NIPSNAP1	cis	cerebellum	SCAN
rs2857645	NIPSNAP1	cis	parietal	SCAN
rs2857645	OSM	cis	cerebellum	SCAN
rs2857645	NEFH	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
4	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
5	chr22:30032200-30070000	Weak transcription	Fetal Brain Male	brain
6	chr22:30037200-30064200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:30038800-30069800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr22:30039000-30068000	Weak transcription	Hela-S3	cervix
9	chr22:30043800-30064000	Weak transcription	Fetal Heart	heart
10	chr22:30048000-30064000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr22:30048000-30064200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr22:30049600-30062000	Strong transcription	HSMM	muscle
13	chr22:30050000-30062400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr22:30050200-30075000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr22:30050200-30084800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr22:30050400-30062800	Strong transcription	Liver	Liver
17	chr22:30050400-30084400	Strong transcription	Left Ventricle	heart
18	chr22:30050400-30093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr22:30050600-30062000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr22:30050800-30084800	Strong transcription	Thymus	Thymus
21	chr22:30051000-30083600	Strong transcription	Fetal Muscle Leg	muscle
22	chr22:30051000-30085400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr22:30051400-30082600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr22:30053000-30062000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr22:30053200-30065600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:30053400-30084400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr22:30053400-30087400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr22:30053800-30081000	Strong transcription	Fetal Intestine Large	intestine
29	chr22:30053800-30084600	Strong transcription	Fetal Stomach	stomach
30	chr22:30054000-30062200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr22:30054000-30094800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr22:30054400-30065200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr22:30054400-30067800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr22:30055000-30063400	Weak transcription	HepG2	liver
35	chr22:30055400-30070800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr22:30055400-30095200	Strong transcription	Fetal Intestine Small	intestine
37	chr22:30056000-30094800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr22:30056200-30070800	Weak transcription	Fetal Kidney	kidney
39	chr22:30056200-30084600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr22:30056200-30084800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr22:30056400-30064400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr22:30056400-30066600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr22:30056400-30084600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr22:30056800-30066400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr22:30057000-30062200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr22:30057600-30063400	Weak transcription	Brain Angular Gyrus	brain
47	chr22:30057800-30064400	Weak transcription	A549	lung
48	chr22:30057800-30085600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr22:30057800-30086000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr22:30058200-30062400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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