Variant report

Variant	rs10038723
Chromosome Location	chr5:74717653-74717654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:74711691..74714209-chr5:74716587..74718777,2	K562	blood:
2	chr5:74712709..74715090-chr5:74716587..74719083,2	K562	blood:
3	chr5:74717369..74719270-chr5:74723978..74725689,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10043621	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10044053	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10053643	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10060260	0.85[EUR][1000 genomes]
rs10067641	0.87[EUR][1000 genomes]
rs10075139	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10434644	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10462517	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10473972	0.87[ASN][1000 genomes]
rs10474433	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs10474434	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10474436	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1051795	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10942739	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11957913	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12234032	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13354407	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1427924	0.87[EUR][1000 genomes]
rs17238484	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17739580	0.87[EUR][1000 genomes]
rs1863934	0.89[EUR][1000 genomes]
rs1863935	0.89[EUR][1000 genomes]
rs2287711	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs28609217	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2878418	0.82[ASN][1000 genomes]
rs2878519	0.89[EUR][1000 genomes]
rs2878520	0.88[EUR][1000 genomes]
rs3213801	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs3761742	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761743	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3846665	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846666	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3931914	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4045166	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4385188	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4440336	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4703670	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4703674	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs4704214	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4704228	0.84[EUR][1000 genomes]
rs57149337	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57312935	0.86[EUR][1000 genomes]
rs5744533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5744555	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5744575	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744598	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744601	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744621	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5744663	0.80[ASN][1000 genomes]
rs59506842	0.85[EUR][1000 genomes]
rs61430233	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6453134	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67969809	0.89[EUR][1000 genomes]
rs6861279	0.87[EUR][1000 genomes]
rs6863398	0.84[ASN][1000 genomes]
rs6872314	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6874781	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6891949	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs698912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73120833	0.86[ASN][1000 genomes]
rs7356637	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7445415	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs767676	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7700468	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7701925	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs7706857	0.87[EUR][1000 genomes]
rs7709282	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs7717505	0.87[EUR][1000 genomes]
rs7723531	0.87[EUR][1000 genomes]
rs7737959	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs924452	0.87[EUR][1000 genomes]
rs9293656	0.87[EUR][1000 genomes]
rs9332464	0.87[EUR][1000 genomes]
rs9885386	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10038723	GCNT4	cis	cerebellum	SCAN
rs10038723	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:74659800-74720600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:74660000-74722800	Weak transcription	Fetal Heart	heart
5	chr5:74667000-74723200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:74670800-74720600	Weak transcription	Right Ventricle	heart
7	chr5:74670800-74731400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:74671000-74722800	Weak transcription	Hela-S3	cervix
9	chr5:74674400-74761400	Weak transcription	Esophagus	oesophagus
10	chr5:74675400-74720800	Weak transcription	Small Intestine	intestine
11	chr5:74676200-74721000	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:74677400-74722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:74677600-74734200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:74677800-74721000	Weak transcription	NH-A	brain
15	chr5:74677800-74725000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:74677800-74731400	Weak transcription	Aorta	Aorta
17	chr5:74678000-74720600	Weak transcription	Colonic Mucosa	Colon
18	chr5:74678000-74730800	Weak transcription	Psoas Muscle	Psoas
19	chr5:74680600-74721000	Weak transcription	HMEC	breast
20	chr5:74680800-74722600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:74681000-74723200	Weak transcription	HUVEC	blood vessel
22	chr5:74681400-74718400	Weak transcription	Brain Germinal Matrix	brain
23	chr5:74681800-74720600	Weak transcription	Fetal Brain Male	brain
24	chr5:74684000-74720400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:74684000-74720800	Weak transcription	Thymus	Thymus
26	chr5:74684000-74731200	Weak transcription	HSMMtube	muscle
27	chr5:74695200-74718200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:74695400-74721000	Weak transcription	Brain Anterior Caudate	brain
29	chr5:74695400-74721000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:74695400-74723200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:74695600-74721000	Weak transcription	Brain Angular Gyrus	brain
32	chr5:74697000-74720400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr5:74699600-74731200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:74702000-74721000	Weak transcription	A549	lung
35	chr5:74703800-74722600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr5:74703800-74723000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr5:74704200-74722000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr5:74704200-74723200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:74705800-74718800	Weak transcription	Left Ventricle	heart
40	chr5:74705800-74719200	Weak transcription	Lung	lung
41	chr5:74706000-74731400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:74706200-74720600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:74706200-74756400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr5:74708000-74722000	Strong transcription	Primary B cells from cord blood	blood
45	chr5:74708200-74720800	Weak transcription	Brain Substantia Nigra	brain
46	chr5:74708200-74721800	Strong transcription	Adipose Nuclei	Adipose
47	chr5:74708400-74720800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:74708400-74725400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:74708400-74746000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr5:74708600-74721000	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links