Variant report

Variant	rs9608885
Chromosome Location	chr22:30738161-30738162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:30735609-30738535	GM12878	blood:	n/a	n/a
2	POLR2A	chr22:30737310-30738304	HepG2	liver:	n/a	n/a
3	POLR2A	chr22:30737799-30738331	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:30738090-30738258	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30736285..30738437-chr22:30751447..30754136,2	K562	blood:
2	chr22:30721434..30723843-chr22:30737479..30740425,2	K562	blood:
3	chr22:30733497..30738627-chr22:30739549..30742352,7	K562	blood:
4	chr22:30736285..30738543-chr22:30751447..30754136,3	K562	blood:

Variant related genes	Relation type
SF3A1	TF binding region
ENSG00000099992	Chromatin interaction
ENSG00000099995	Chromatin interaction
ENSG00000187860	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1002189	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1076295	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1076297	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1076298	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1076299	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11705092	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11912350	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11913885	0.88[AFR][1000 genomes]
rs13053375	1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs13053595	0.88[AFR][1000 genomes]
rs13054303	0.88[AFR][1000 genomes]
rs13055431	0.88[AFR][1000 genomes]
rs13056326	0.88[AFR][1000 genomes]
rs13057340	0.88[AFR][1000 genomes]
rs13057861	0.88[AFR][1000 genomes]
rs17656850	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17657174	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs17657653	0.85[AFR][1000 genomes]
rs17657701	0.88[AFR][1000 genomes]
rs17658238	0.85[AFR][1000 genomes]
rs17658686	0.80[CHD][hapmap]
rs17730485	0.88[AFR][1000 genomes]
rs17730538	0.88[AFR][1000 genomes]
rs17736937	0.85[AFR][1000 genomes]
rs1990268	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2097919	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2229807	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2240345	0.81[ASW][hapmap]
rs2240420	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2412986	0.81[ASW][hapmap]
rs28360656	0.88[AFR][1000 genomes]
rs34995457	0.82[AFR][1000 genomes]
rs35293738	0.88[AFR][1000 genomes]
rs35537171	0.88[AFR][1000 genomes]
rs35711436	0.84[AFR][1000 genomes]
rs35782599	0.88[AFR][1000 genomes]
rs4390846	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4820005	0.88[AFR][1000 genomes]
rs4820006	0.85[AFR][1000 genomes]
rs4820007	0.88[AFR][1000 genomes]
rs4820835	0.85[AFR][1000 genomes]
rs4820836	0.88[AFR][1000 genomes]
rs4820838	0.85[AFR][1000 genomes]
rs4820839	0.85[AFR][1000 genomes]
rs4820845	0.81[CHD][hapmap]
rs4823089	0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs5749062	0.88[AFR][1000 genomes]
rs5749063	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs5749067	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs5749075	0.88[AFR][1000 genomes]
rs5749076	0.88[AFR][1000 genomes]
rs5749077	0.88[AFR][1000 genomes]
rs5749080	1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs5749081	0.97[LWK][hapmap];1.00[MKK][hapmap];0.88[AFR][1000 genomes]
rs5749087	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs5749089	0.93[ASN][1000 genomes]
rs5749104	0.81[ASW][hapmap]
rs5753060	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs5753061	0.85[AFR][1000 genomes]
rs5753070	0.85[AFR][1000 genomes]
rs5753073	0.88[AFR][1000 genomes]
rs5753078	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs5753095	0.88[AFR][1000 genomes]
rs5753096	0.85[AFR][1000 genomes]
rs5753097	0.88[AFR][1000 genomes]
rs5753101	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs5753103	0.92[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs5753105	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs5753106	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs5753110	0.85[AFR][1000 genomes]
rs5753161	0.81[ASW][hapmap]
rs5763928	0.86[MKK][hapmap]
rs5763939	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5994293	0.92[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs5997602	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs5997623	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61322750	0.88[AFR][1000 genomes]
rs7287175	0.85[AFR][1000 genomes]
rs7287908	0.88[AFR][1000 genomes]
rs7288947	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs737750	0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs737751	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs737813	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs737948	0.86[MKK][hapmap]
rs740220	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs740221	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740222	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs740223	0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs757663	0.81[ASW][hapmap]
rs757868	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs8136826	0.88[AFR][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	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	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv3593	chr22:30705980-30751122	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
5	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
6	nsv1064350	chr22:30724148-30742125	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	n/a
7	nsv1066179	chr22:30724148-30766466	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9608885	NIPSNAP1	cis	cerebellum	SCAN
rs9608885	CRYBB2	cis	parietal	SCAN
rs9608885	CABP7	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30723600-30751600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:30723800-30742800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:30724400-30750000	Strong transcription	Thymus	Thymus
4	chr22:30724600-30750200	Strong transcription	Osteobl	bone
5	chr22:30724800-30745200	Strong transcription	NHEK	skin
6	chr22:30724800-30750200	Strong transcription	Fetal Intestine Small	intestine
7	chr22:30725400-30743400	Strong transcription	Fetal Stomach	stomach
8	chr22:30725400-30749600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr22:30725400-30750000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr22:30725600-30743600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr22:30725600-30744200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr22:30725600-30750200	Strong transcription	Fetal Intestine Large	intestine
13	chr22:30725800-30740600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr22:30725800-30742600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr22:30725800-30743200	Strong transcription	Fetal Thymus	thymus
16	chr22:30725800-30748000	Strong transcription	Dnd41	blood
17	chr22:30726000-30743200	Strong transcription	Fetal Lung	lung
18	chr22:30726400-30740400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr22:30726400-30745400	Strong transcription	HSMM	muscle
20	chr22:30726400-30747000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr22:30726400-30749600	Strong transcription	Fetal Brain Female	brain
22	chr22:30726400-30749600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr22:30726400-30750200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr22:30726400-30750200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr22:30726600-30740400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr22:30726600-30743000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr22:30726600-30743000	Strong transcription	Lung	lung
28	chr22:30726600-30743400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr22:30726600-30743400	Strong transcription	GM12878-XiMat	blood
30	chr22:30726600-30743600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr22:30726600-30744000	Strong transcription	Rectal Smooth Muscle	rectum
32	chr22:30726600-30744600	Strong transcription	Primary T cells from cord blood	blood
33	chr22:30726600-30744600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr22:30726600-30749200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr22:30726600-30749600	Strong transcription	Primary B cells from cord blood	blood
36	chr22:30726600-30749800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:30726600-30750000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr22:30726600-30750000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr22:30726600-30750200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr22:30726600-30750400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:30726600-30750400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr22:30726600-30750400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr22:30726600-30750600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr22:30726600-30750600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr22:30726600-30750800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr22:30726600-30750800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr22:30726800-30740800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr22:30726800-30743200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr22:30726800-30749000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr22:30726800-30749200	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links