Variant report

Variant	rs9552
Chromosome Location	chr5:112929694-112929695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112923262..112928429-chr5:112929075..112932971,5	K562	blood:

Variant related genes	Relation type
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10045444	0.82[AMR][1000 genomes]
rs10071966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1035408	0.80[EUR][1000 genomes]
rs1132528	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11957650	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12659978	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs164251	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs1820056	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs182987	0.85[EUR][1000 genomes]
rs2303717	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2416282	0.82[ASW][hapmap];0.88[MEX][hapmap]
rs2431548	0.85[EUR][1000 genomes]
rs2434665	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs255856	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs26985	0.88[JPT][hapmap]
rs27566	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs2910018	0.96[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2914200	0.86[AMR][1000 genomes]
rs348933	0.85[EUR][1000 genomes]
rs3763139	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3857437	0.89[CHB][hapmap]
rs3906371	0.87[CHD][hapmap];0.91[MEX][hapmap]
rs3936062	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs423089	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs4235796	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4398627	0.83[MEX][hapmap]
rs4415069	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4438867	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4444963	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs459428	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs461034	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs463216	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs4639215	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs465898	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs466564	0.88[JPT][hapmap]
rs4705830	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57617774	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59958489	0.80[AMR][1000 genomes]
rs62373764	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6594736	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66534827	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs675353	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap]
rs6881976	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6886338	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7702120	0.94[JPT][hapmap]
rs7702405	0.87[EUR][1000 genomes]
rs7703233	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7713378	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326895	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9885084	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882721	chr5:112859994-112963488	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv882724	chr5:112868878-112933202	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv1033202	chr5:112891857-112945992	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv520674	chr5:112911165-112942820	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	esv2752057	chr5:112916398-112945992	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv1029507	chr5:112916398-112945992	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv2763910	chr5:112916398-112951827	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv1031336	chr5:112916398-112956588	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
9	esv3402243	chr5:112929338-112929744	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9552	LILRP2	trans	parietal	SCAN
rs9552	YTHDC2	cis	parietal	SCAN
rs9552	YTHDC2	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112867400-112933000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:112870200-112930800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:112889400-112930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:112904600-112934800	Weak transcription	Psoas Muscle	Psoas
5	chr5:112907400-112932000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:112908800-112935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:112910600-112933400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:112910600-112935200	Weak transcription	Spleen	Spleen
9	chr5:112910600-112935400	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:112910600-112936600	Weak transcription	Colonic Mucosa	Colon
11	chr5:112910600-112942000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:112910800-112930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:112910800-112933600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:112910800-112933600	Weak transcription	Fetal Stomach	stomach
15	chr5:112910800-112934600	Weak transcription	Gastric	stomach
16	chr5:112910800-112935000	Weak transcription	Pancreas	Pancrea
17	chr5:112910800-112935200	Weak transcription	Esophagus	oesophagus
18	chr5:112910800-112937400	Weak transcription	Fetal Intestine Small	intestine
19	chr5:112910800-112938200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:112910800-112942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:112911000-112930000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:112916000-112931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:112916400-112930400	Weak transcription	NHLF	lung
24	chr5:112916400-112933000	Weak transcription	Thymus	Thymus
25	chr5:112916400-112933400	Weak transcription	Aorta	Aorta
26	chr5:112916800-112936000	Weak transcription	Fetal Heart	heart
27	chr5:112917200-112942000	Weak transcription	K562	blood
28	chr5:112917400-112937600	Weak transcription	HSMMtube	muscle
29	chr5:112917800-112933400	Weak transcription	Brain Angular Gyrus	brain
30	chr5:112918000-112933600	Weak transcription	Hela-S3	cervix
31	chr5:112918000-112939000	Weak transcription	NHEK	skin
32	chr5:112920400-112939000	Weak transcription	HMEC	breast
33	chr5:112920600-112934600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:112920600-112934800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:112920600-112936000	Weak transcription	Brain Anterior Caudate	brain
36	chr5:112920800-112930200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:112920800-112934000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:112920800-112938600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:112920800-112942000	Weak transcription	Ovary	ovary
40	chr5:112922000-112933400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:112923600-112933600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr5:112924600-112930800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr5:112924800-112931800	Strong transcription	Dnd41	blood
44	chr5:112924800-112933000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:112925200-112930200	Strong transcription	Adipose Nuclei	Adipose
46	chr5:112925200-112931000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:112925200-112932400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:112925400-112930600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr5:112925600-112930200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr5:112925600-112930600	Strong transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links