Variant report

Variant	rs17371159
Chromosome Location	chr1:179972337-179972338
allele	A/C
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	FOXM1	chr1:179972269-179972876	GM12878	blood:	n/a	n/a
2	RCOR1	chr1:179972328-179972840	GM12878	blood:	n/a	n/a
3	EBF1	chr1:179972295-179972761	GM12878	blood:	n/a	n/a
4	RUNX3	chr1:179972297-179972830	GM12878	blood:	n/a	n/a
5	MAX	chr1:179972310-179972705	GM12878	blood:	n/a	n/a
6	NFIC	chr1:179972221-179972992	GM12878	blood:	n/a	n/a
7	RELA	chr1:179972304-179972853	GM19099	blood:	n/a	n/a
8	ATF2	chr1:179972174-179972960	GM12878	blood:	n/a	n/a
9	MEF2A	chr1:179972101-179973093	GM12878	blood:	n/a	chr1:179972599-179972614 chr1:179972638-179972653 chr1:179972637-179972658 chr1:179972596-179972617 chr1:179972599-179972616 chr1:179972637-179972658 chr1:179972638-179972654 chr1:179972642-179972651 chr1:179972641-179972652 chr1:179972638-179972653 chr1:179972639-179972654 chr1:179972600-179972615 chr1:179972640-179972651 chr1:179972640-179972655 chr1:179972639-179972653 chr1:179972601-179972616 chr1:179972638-179972655
10	MEF2C	chr1:179972230-179972936	GM12878	blood:	n/a	chr1:179972599-179972614 chr1:179972599-179972614 chr1:179972638-179972653 chr1:179972637-179972658 chr1:179972596-179972617 chr1:179972599-179972616 chr1:179972637-179972658 chr1:179972638-179972654 chr1:179972642-179972651 chr1:179972641-179972652 chr1:179972638-179972653 chr1:179972639-179972654 chr1:179972600-179972615 chr1:179972640-179972651 chr1:179972640-179972655 chr1:179972639-179972653 chr1:179972601-179972616 chr1:179972638-179972655
11	RELA	chr1:179972305-179973025	GM12878	blood:	n/a	n/a
12	STAT3	chr1:179972324-179972789	GM12878	blood:	n/a	n/a
13	MXI1	chr1:179972290-179972490	GM12878	blood:	n/a	n/a
14	BCLAF1	chr1:179972185-179972836	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179849513..179851721-chr1:179972324..179974265,2	K562	blood:

Variant related genes	Relation type
ENSG00000223450	TF binding region
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1048418	1.00[CHD][hapmap]
rs10913920	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913939	1.00[CHB][hapmap]
rs12091464	1.00[CHB][hapmap]
rs12116940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118265	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12119130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121845	0.84[TSI][hapmap]
rs12123560	0.84[TSI][hapmap]
rs12125245	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125592	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126496	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12126967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127784	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129115	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130397	0.84[EUR][1000 genomes]
rs12130673	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132694	0.84[TSI][hapmap]
rs12133136	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135828	0.84[EUR][1000 genomes]
rs12136091	1.00[CHB][hapmap]
rs12138429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139323	0.84[TSI][hapmap]
rs12140589	0.84[EUR][1000 genomes]
rs12140622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142457	1.00[CHB][hapmap]
rs12144328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144346	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855021	0.84[TSI][hapmap]
rs16855022	0.84[TSI][hapmap]
rs16855025	0.84[TSI][hapmap]
rs16855048	0.84[TSI][hapmap]
rs16855070	0.84[EUR][1000 genomes]
rs16855107	0.84[TSI][hapmap]
rs16855110	0.84[TSI][hapmap]
rs16855125	0.80[CEU][hapmap]
rs16855130	0.84[TSI][hapmap]
rs17299006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371308	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17855475	1.00[CHB][hapmap]
rs1801795	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845388	1.00[CHD][hapmap]
rs3856049	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889149	1.00[CHB][hapmap]
rs4301600	1.00[CHD][hapmap]
rs59132689	0.82[EUR][1000 genomes]
rs73032390	0.82[EUR][1000 genomes]
rs9701232	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701237	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17371159	RALGPS2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179938000-179983200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:179938600-179975800	Weak transcription	Thymus	Thymus
3	chr1:179938600-179983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:179938600-179984600	Weak transcription	Lung	lung
5	chr1:179939000-179989000	Weak transcription	Gastric	stomach
6	chr1:179939800-179974800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
8	chr1:179946400-179972800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:179946400-179983000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:179946400-179989200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:179946600-179983200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:179947800-179989400	Weak transcription	Small Intestine	intestine
13	chr1:179948600-179983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:179949400-179980600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:179950000-179980600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:179951400-179974600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:179951800-179974800	Weak transcription	Hela-S3	cervix
18	chr1:179954200-179975400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:179954600-179975600	Weak transcription	Fetal Kidney	kidney
20	chr1:179955000-179989200	Weak transcription	Aorta	Aorta
21	chr1:179955800-179983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:179956800-179989400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:179957000-179975800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:179957800-179972400	Weak transcription	Brain Anterior Caudate	brain
25	chr1:179958600-179991600	Weak transcription	Fetal Brain Male	brain
26	chr1:179958800-179978000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:179959200-179983200	Weak transcription	NHLF	lung
28	chr1:179959600-179983000	Weak transcription	Colonic Mucosa	Colon
29	chr1:179962000-179989200	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:179962400-179983200	Weak transcription	A549	lung
31	chr1:179963600-179975800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:179964000-179989200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:179964000-180014200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:179964200-179975400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:179964400-179984600	Weak transcription	HUVEC	blood vessel
36	chr1:179964600-179984200	Weak transcription	Fetal Intestine Small	intestine
37	chr1:179965000-179978000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:179965800-180013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:179966400-179972400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:179966400-179973200	Weak transcription	Fetal Lung	lung
41	chr1:179966400-179973400	Weak transcription	Brain Substantia Nigra	brain
42	chr1:179966400-179974000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:179966400-179974800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:179966400-179974800	Weak transcription	K562	blood
45	chr1:179966400-179981000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:179966400-179981600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:179966400-179983200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:179966400-179983200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:179966600-179973200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:179966600-179973400	Weak transcription	Adipose Nuclei	Adipose

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