Variant report

Variant	rs7497342
Chromosome Location	chr15:74948063-74948064
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	chr15:74909966..74912107-chr15:74947107..74949319,2	K562	blood:

Variant related genes	Relation type
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10459601	0.82[GIH][hapmap]
rs10459648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs10851871	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs10851873	0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs11072492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs11072493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072494	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11072495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11072496	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072497	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072499	0.87[GIH][hapmap]
rs11629749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11629946	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12437519	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12439113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12441932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12442013	0.85[ASN][1000 genomes]
rs12442097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12594447	0.81[ASN][1000 genomes]
rs1456432	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16969247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16969393	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2068982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2198843	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2415241	0.86[ASN][1000 genomes]
rs2415242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs2415245	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4073149	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs4128436	0.93[YRI][hapmap]
rs4646421	0.82[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs4886601	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4887152	0.89[CEU][hapmap]
rs4887154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4887159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs4887160	0.85[ASN][1000 genomes]
rs4887162	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4887163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4887165	0.85[ASN][1000 genomes]
rs4887166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58473469	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6495105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6495106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6495112	0.82[GIH][hapmap]
rs6495115	0.86[ASN][1000 genomes]
rs6495116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs6495117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6495118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6495119	0.87[GIH][hapmap]
rs6495121	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7161903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166701	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs7171838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs7176095	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7177407	0.85[ASN][1000 genomes]
rs7178568	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74025818	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7497036	0.82[GIH][hapmap]
rs8023479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8023865	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8026923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs8027066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8028163	0.81[ASN][1000 genomes]
rs8028430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs8029116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs8029215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs8037714	0.81[ASN][1000 genomes]
rs8040745	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8041030	0.82[ASN][1000 genomes]
rs8041807	0.81[ASN][1000 genomes]
rs8043082	0.86[ASN][1000 genomes]
rs9635320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9672559	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9888684	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1812223	chr15:74869438-74948063	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv1814078	chr15:74884447-74948063	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv457204	chr15:74885091-74948063	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv569991	chr15:74885091-74948063	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv817698	chr15:74889163-75019449	Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7497342	RPLP1	cis	parietal	SCAN
rs7497342	SEMA7A	cis	cerebellum	SCAN
rs7497342	ARIH1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74921800-74963400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:74929200-74963400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr15:74933000-74956200	Weak transcription	A549	lung
4	chr15:74933200-74963400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:74933400-74963200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:74934000-74955800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:74934400-74962400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:74935400-74963400	Weak transcription	Aorta	Aorta
9	chr15:74936000-74950200	Weak transcription	Gastric	stomach
10	chr15:74936000-74963000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:74936000-74968800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:74936200-74956200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:74936200-74956400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:74936200-74963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:74936400-74956200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:74936600-74956200	Weak transcription	Spleen	Spleen
17	chr15:74938800-74960200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:74940400-74949400	Weak transcription	Esophagus	oesophagus
19	chr15:74941000-74954400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:74941200-74963000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:74941800-74948400	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:74941800-74951000	Enhancers	Fetal Heart	heart
23	chr15:74942000-74949600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:74942200-74948400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:74942400-74948800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:74942400-74950600	Enhancers	Brain Hippocampus Middle	brain
27	chr15:74943000-74958800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:74943400-74948800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:74943600-74948600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:74945400-74948200	Enhancers	HSMMtube	muscle
31	chr15:74945400-74948800	Strong transcription	Primary T cells from cord blood	blood
32	chr15:74945400-74951000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:74945600-74948200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr15:74945600-74948400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:74945600-74948400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:74945600-74948400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:74945600-74948400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr15:74945600-74948400	Strong transcription	HepG2	liver
39	chr15:74945600-74948600	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr15:74945600-74948600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:74945600-74948800	Strong transcription	Dnd41	blood
42	chr15:74945600-74950400	Enhancers	Fetal Brain Male	brain
43	chr15:74945600-74950600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:74945600-74950600	Enhancers	Brain Angular Gyrus	brain
45	chr15:74945600-74950600	Enhancers	Brain Substantia Nigra	brain
46	chr15:74945600-74951600	Enhancers	NH-A	brain
47	chr15:74946000-74948400	Weak transcription	Lung	lung
48	chr15:74946000-74948600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:74946000-74956200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:74946000-74962600	Weak transcription	Placenta Amnion	Placenta Amnion

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