Variant report

Variant	rs9942965
Chromosome Location	chr9:95737649-95737650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUSD3-4	chr9:95737520-95737687	NONHSAT133224
2	lnc-SUSD3-4	chr9:95737520-95737687	NONHSAT133225

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10121856	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10283714	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10761189	0.95[JPT][hapmap]
rs10821046	0.90[GIH][hapmap]
rs10821048	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821049	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821050	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821051	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992561	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992562	0.80[AMR][1000 genomes]
rs10992564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788120	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300085	0.95[JPT][hapmap]
rs3802381	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3936099	0.90[GIH][hapmap]
rs4302906	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744159	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4744161	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479445	0.95[JPT][hapmap]
rs7026624	0.95[GIH][hapmap]
rs7030160	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7032953	0.82[EUR][1000 genomes]
rs7847879	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7848528	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850247	0.82[CEU][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs7867742	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7869056	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7869421	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7870077	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7875497	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9942903	1.00[CEU][hapmap];0.95[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];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9942965	ZNF484	cis	cerebellum	SCAN
rs9942965	ZNF484	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95728200-95739600	Weak transcription	Fetal Stomach	stomach
2	chr9:95728800-95739400	Weak transcription	Gastric	stomach
3	chr9:95728800-95739600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:95728800-95740600	Weak transcription	Small Intestine	intestine
5	chr9:95729000-95739400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:95729000-95741400	Weak transcription	Right Ventricle	heart
7	chr9:95729200-95739200	Weak transcription	Colonic Mucosa	Colon
8	chr9:95732000-95741200	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:95733400-95741400	Weak transcription	Fetal Brain Female	brain
10	chr9:95733400-95742000	Weak transcription	Fetal Brain Male	brain
11	chr9:95733600-95738000	Weak transcription	Esophagus	oesophagus
12	chr9:95733800-95739400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:95734200-95737800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:95735000-95739800	Enhancers	Placenta	Placenta
15	chr9:95735400-95752600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr9:95735600-95740200	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr9:95735800-95739600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:95735800-95739600	Strong transcription	Fetal Thymus	thymus
19	chr9:95735800-95740000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:95735800-95740200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:95735800-95740200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:95735800-95740400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:95735800-95742200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr9:95736000-95740200	Strong transcription	Primary hematopoietic stem cells	blood
25	chr9:95736000-95741600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:95736200-95737800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
27	chr9:95736200-95740200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr9:95736200-95740400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr9:95736200-95740400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr9:95736400-95739000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr9:95736400-95739400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr9:95736400-95739600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:95736400-95740200	Genic enhancers	Primary T cells from cord blood	blood
34	chr9:95736600-95738200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr9:95736600-95740200	Strong transcription	Thymus	Thymus
36	chr9:95736600-95740400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr9:95736800-95738600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:95736800-95738600	Strong transcription	Spleen	Spleen
39	chr9:95736800-95740200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr9:95736800-95740200	Strong transcription	Dnd41	blood
41	chr9:95736800-95740400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr9:95736800-95743200	Weak transcription	Stomach Mucosa	stomach
43	chr9:95737000-95738400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr9:95737000-95739000	Strong transcription	Primary B cells from cord blood	blood
45	chr9:95737200-95740200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:95737200-95740400	Strong transcription	Brain Germinal Matrix	brain
47	chr9:95737400-95737800	Weak transcription	Lung	lung
48	chr9:95737400-95737800	Enhancers	Pancreas	Pancrea
49	chr9:95737400-95738000	Genic enhancers	Fetal Intestine Small	intestine
50	chr9:95737400-95738400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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