Variant report

Variant	rs1171509
Chromosome Location	chr10:22960199-22960200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:22957083..22958946-chr10:22960169..22962668,2	K562	blood:
2	chr10:22959644..22961517-chr10:22966736..22968409,2	K562	blood:
3	chr10:22953483..22956745-chr10:22958221..22961300,4	K562	blood:
4	chr10:22960188..22962798-chr10:23001750..23003397,2	K562	blood:

Variant related genes	Relation type
ENSG00000150867	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10764339	1.00[CHB][hapmap]
rs10764344	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs10828323	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10828324	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10828325	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs10828328	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11013052	1.00[CHB][hapmap]
rs11013066	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11013067	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11013068	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11013077	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11013082	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11013091	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1171489	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1171490	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1171492	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap]
rs1171497	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1171499	0.81[EUR][1000 genomes]
rs1171503	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs1171504	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs1171506	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12246676	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12253847	1.00[CHB][hapmap]
rs12354766	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12356117	1.00[CHB][hapmap]
rs12357289	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12357384	1.00[CHB][hapmap]
rs12357444	1.00[CHB][hapmap]
rs12358560	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12770214	1.00[CHB][hapmap]
rs12774725	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1343504	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs1359641	0.87[YRI][hapmap]
rs1359643	0.87[YRI][hapmap]
rs1409393	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs1409394	0.80[AMR][1000 genomes]
rs1409395	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes]
rs1614387	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[TSI][hapmap]
rs1627549	0.87[YRI][hapmap]
rs16922592	0.93[YRI][hapmap]
rs1750747	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs1750748	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1750764	0.86[YRI][hapmap]
rs1750765	0.87[YRI][hapmap]
rs1750766	0.81[YRI][hapmap]
rs1750768	0.87[YRI][hapmap]
rs1750775	0.84[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap]
rs1750777	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs1778306	0.82[AFR][1000 genomes]
rs1778309	0.81[YRI][hapmap]
rs1778313	0.84[YRI][hapmap]
rs1778321	0.81[YRI][hapmap]
rs1778322	0.87[YRI][hapmap]
rs1778334	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1778335	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs1778338	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs1778339	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs1778340	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs1778342	0.92[CEU][hapmap]
rs1778345	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1778346	1.00[CHB][hapmap]
rs1778347	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap]
rs2031620	0.82[CHB][hapmap]
rs2154053	0.84[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap]
rs2559534	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2798981	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs7071306	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7895928	0.83[CHD][hapmap]
rs7912132	0.82[CHB][hapmap]
rs7921549	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs943196	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs943197	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830947	chr10:22881196-23004381	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv831809	chr10:22918101-23069676	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1171509	PIP4K2A	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22946200-22961600	Weak transcription	Aorta	Aorta
2	chr10:22948000-22961400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:22949000-22965000	Weak transcription	Right Atrium	heart
4	chr10:22949200-22969600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:22949800-22960600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:22950000-22961400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:22952000-22963000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr10:22952000-22970200	Weak transcription	Esophagus	oesophagus
9	chr10:22952200-22960400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:22952400-22961400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr10:22952400-22970000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:22955800-22962800	Weak transcription	Fetal Kidney	kidney
13	chr10:22955800-22970200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:22956000-22960200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:22956000-22970400	Weak transcription	NHLF	lung
16	chr10:22956200-22961600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:22956200-22968200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr10:22956200-22970200	Weak transcription	Liver	Liver
19	chr10:22956400-22961400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:22956800-22967000	Enhancers	Brain Cingulate Gyrus	brain
21	chr10:22956800-22971600	Weak transcription	Primary B cells from cord blood	blood
22	chr10:22957000-22961000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:22957200-22961800	Weak transcription	Lung	lung
24	chr10:22957400-22963200	Enhancers	Brain Germinal Matrix	brain
25	chr10:22958000-22963600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr10:22958200-22962800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:22958200-22965200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr10:22958200-22967200	Enhancers	Brain Anterior Caudate	brain
29	chr10:22958400-22972200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr10:22958600-22960200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr10:22958600-22961600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr10:22958600-22961600	Weak transcription	HepG2	liver
33	chr10:22958600-22961800	Weak transcription	Psoas Muscle	Psoas
34	chr10:22958600-22971000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr10:22958600-22975400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr10:22958800-22960200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr10:22958800-22960200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:22958800-22960200	Weak transcription	Small Intestine	intestine
39	chr10:22958800-22960400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr10:22958800-22960400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr10:22958800-22960400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr10:22958800-22961000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:22958800-22961200	Enhancers	K562	blood
44	chr10:22958800-22961400	Weak transcription	A549	lung
45	chr10:22958800-22961600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr10:22958800-22961600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr10:22958800-22961600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr10:22958800-22968400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr10:22958800-22969800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:22958800-22969800	Weak transcription	Left Ventricle	heart

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