Variant report

Variant	rs2307113
Chromosome Location	chr5:74998264-74998265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74997231..74999217-chr5:75000460..75002166,2	K562	blood:
2	chr5:74996831..74999207-chr5:75004311..75007242,2	K562	blood:

Variant related genes	Relation type
ENSG00000207333	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10462356	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10462521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515213	0.87[CHD][hapmap]
rs11746063	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11748378	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166183	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563877	0.87[CHD][hapmap]
rs17649055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649248	0.87[CHD][hapmap]
rs17649266	0.87[CHD][hapmap]
rs17649350	0.87[CHD][hapmap]
rs1817869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193344	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194137	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047059	0.91[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2291630	0.87[CHD][hapmap]
rs253388	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs253389	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34905687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797580	0.83[CEU][hapmap]
rs40059	0.84[EUR][1000 genomes]
rs41534344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703678	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4703679	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703680	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704234	1.00[CEU][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59778668	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60134294	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60423072	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61173369	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66493518	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67054144	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67803720	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868069	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633978	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633979	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7381033	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv830353	chr5:74961520-75152609	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2307113	DMGDH	cis	parietal	SCAN
rs2307113	TNPO1	cis	cerebellum	SCAN
rs2307113	HMGCR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74965200-75011800	Weak transcription	Brain Germinal Matrix	brain
2	chr5:74965400-75012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:74965400-75012400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:74965400-75012400	Weak transcription	Right Ventricle	heart
5	chr5:74965600-75010400	Weak transcription	Gastric	stomach
6	chr5:74965600-75011400	Weak transcription	Small Intestine	intestine
7	chr5:74966000-74998400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:74968800-74998400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:74971200-75012400	Weak transcription	Aorta	Aorta
10	chr5:74971200-75012400	Weak transcription	Brain Substantia Nigra	brain
11	chr5:74979000-75003800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:74979800-74998400	Weak transcription	Ovary	ovary
13	chr5:74980000-75012200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr5:74981400-74999200	Weak transcription	Fetal Stomach	stomach
15	chr5:74981400-74999600	Weak transcription	Fetal Intestine Small	intestine
16	chr5:74981400-75002600	Weak transcription	Pancreas	Pancrea
17	chr5:74984200-75012400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:74985400-74998400	Weak transcription	HSMM	muscle
19	chr5:74986400-74998400	Weak transcription	Left Ventricle	heart
20	chr5:74986800-74998400	Weak transcription	NH-A	brain
21	chr5:74986800-75000000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr5:74986800-75005800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:74987800-75002600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:74990000-75012000	Weak transcription	HSMMtube	muscle
25	chr5:74990000-75012400	Weak transcription	Esophagus	oesophagus
26	chr5:74990200-74998600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr5:74992000-75012400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:74992400-74998400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:74992400-75005800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:74992600-75012600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:74996400-75006400	Weak transcription	Stomach Mucosa	stomach
32	chr5:74996800-75012400	Weak transcription	Fetal Brain Male	brain
33	chr5:74997600-74998400	Strong transcription	HepG2	liver
34	chr5:74997600-74998600	ZNF genes & repeats	GM12878-XiMat	blood
35	chr5:74997600-74998600	Strong transcription	NHLF	lung
36	chr5:74997600-74998800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:74997600-74998800	Strong transcription	Fetal Intestine Large	intestine
38	chr5:74997600-74998800	Strong transcription	Fetal Kidney	kidney
39	chr5:74997600-74999000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr5:74997600-74999000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:74997600-74999000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:74997600-74999000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:74997600-74999000	Strong transcription	Adipose Nuclei	Adipose
44	chr5:74997600-74999000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:74997600-74999000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr5:74997600-74999000	Strong transcription	Rectal Smooth Muscle	rectum
47	chr5:74997600-74999000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr5:74997600-74999000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr5:74997600-74999000	Strong transcription	NHEK	skin
50	chr5:74997600-74999200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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