Variant report

Variant	rs2857641
Chromosome Location	chr22:30057574-30057575
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	0.85[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes]
rs1476757	0.85[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes]
rs2071622	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245185	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245415	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267150	0.85[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2267151	1.00[ASW][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2283863	0.85[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2283864	0.97[AFR][1000 genomes]
rs2527337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530667	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530669	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530670	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530672	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2530673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530675	0.85[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2530676	0.89[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2531850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857637	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857640	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857642	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857645	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]
rs2857648	0.84[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs2857650	0.85[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes]
rs2857651	1.00[ASW][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs5752953	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs5763409	0.99[AFR][1000 genomes]
rs5763422	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs5763431	0.95[AFR][1000 genomes]
rs7291645	0.89[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.82[AFR][1000 genomes]
rs737931	0.85[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9608806	0.93[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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2857641	PITPNB	cis	cerebellum	SCAN
rs2857641	NEFH	cis	cerebellum	SCAN
rs2857641	NIPSNAP1	cis	lymphoblastoid	seeQTL
rs2857641	NIPSNAP1	cis	parietal	SCAN
rs2857641	NIPSNAP1	cis	multi-tissue	Pritchard
rs2857641	NIPSNAP1	cis	cerebellum	SCAN
rs2857641	XBP1	cis	cerebellum	SCAN

Chromatin state (count:122 , 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	chr22:30034400-30060400	Weak transcription	K562	blood
7	chr22:30035400-30060800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr22:30037200-30064200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr22:30038400-30060600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr22:30038800-30069800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr22:30039000-30068000	Weak transcription	Hela-S3	cervix
12	chr22:30043800-30064000	Weak transcription	Fetal Heart	heart
13	chr22:30044800-30058200	Weak transcription	Right Ventricle	heart
14	chr22:30044800-30059600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr22:30045000-30060600	Weak transcription	Brain Substantia Nigra	brain
16	chr22:30047800-30057600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr22:30048000-30064000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr22:30048000-30064200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr22:30049600-30061000	Strong transcription	Dnd41	blood
20	chr22:30049600-30062000	Strong transcription	HSMM	muscle
21	chr22:30050000-30062400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr22:30050200-30061800	Strong transcription	Primary T cells from cord blood	blood
23	chr22:30050200-30075000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr22:30050200-30084800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr22:30050400-30061200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr22:30050400-30061800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr22:30050400-30062800	Strong transcription	Liver	Liver
28	chr22:30050400-30084400	Strong transcription	Left Ventricle	heart
29	chr22:30050400-30093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr22:30050600-30062000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:30050800-30061000	Strong transcription	Adipose Nuclei	Adipose
32	chr22:30050800-30061400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr22:30050800-30084800	Strong transcription	Thymus	Thymus
34	chr22:30051000-30083600	Strong transcription	Fetal Muscle Leg	muscle
35	chr22:30051000-30085400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr22:30051200-30057800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr22:30051400-30082600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr22:30052000-30061600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr22:30052400-30058600	Weak transcription	Brain Germinal Matrix	brain
40	chr22:30052600-30061000	Strong transcription	GM12878-XiMat	blood
41	chr22:30053000-30061000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr22:30053000-30061000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr22:30053000-30061000	Strong transcription	Fetal Lung	lung
44	chr22:30053000-30062000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr22:30053200-30058600	Strong transcription	Fetal Thymus	thymus
46	chr22:30053200-30065600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr22:30053400-30061000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr22:30053400-30084400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr22:30053400-30087400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr22:30053800-30059800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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