Variant report

Variant	rs3776588
Chromosome Location	chr5:36983642-36983643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:36982523..36985797-chr5:36985897..36989039,3	K562	blood:
2	chr5:36979203..36982071-chr5:36982407..36984591,2	MCF-7	breast:
3	chr5:36980854..36983652-chr5:37007051..37009220,2	K562	blood:
4	chr5:36870958..36873840-chr5:36982182..36984989,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10056009	0.87[CEU][hapmap]
rs10072064	0.87[CEU][hapmap]
rs10076911	0.87[CEU][hapmap]
rs10805625	0.87[CEU][hapmap]
rs10941319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11743833	0.86[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11744960	0.88[ASN][1000 genomes]
rs11745128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11958752	0.87[CEU][hapmap]
rs12153359	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12187383	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188075	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12513653	0.88[ASN][1000 genomes]
rs12516349	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12520272	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12520324	0.88[ASN][1000 genomes]
rs12520562	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12521488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16903365	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16903373	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16903403	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16903413	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16903419	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16903427	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16903429	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16903442	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16903456	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16903466	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16903469	0.88[AMR][1000 genomes]
rs16903477	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16903526	0.87[CEU][hapmap]
rs2365495	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2365838	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365910	0.87[CEU][hapmap]
rs300052	0.81[EUR][1000 genomes]
rs301862	0.87[CEU][hapmap]
rs301870	0.87[CEU][hapmap]
rs301890	0.87[CEU][hapmap]
rs301891	0.87[CEU][hapmap]
rs301892	0.87[CEU][hapmap]
rs301893	0.87[CEU][hapmap]
rs301895	0.87[CEU][hapmap]
rs301904	0.86[CEU][hapmap]
rs3822471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849756	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56680779	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56999464	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57686895	0.88[ASN][1000 genomes]
rs60633925	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60643425	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60730034	0.94[ASN][1000 genomes]
rs61638663	0.90[ASN][1000 genomes]
rs62654863	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897283	0.87[CEU][hapmap]
rs7724454	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv1033562	chr5:36927652-36994811	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1023362	chr5:36927652-37010749	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
10	nsv1017947	chr5:36927652-37017180	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
11	nsv1029936	chr5:36927652-37025871	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
12	nsv1029319	chr5:36928654-37017180	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
13	nsv1030883	chr5:36932448-37039857	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
14	esv1803659	chr5:36935129-37039857	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
15	nsv1034694	chr5:36946454-36991605	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1015172	chr5:36946454-36993280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1033778	chr5:36946454-36994811	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1033928	chr5:36947293-37039857	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
19	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active 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	3 gene(s)	inside rSNPs	diseases
20	nsv881592	chr5:36954812-37027258	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
21	esv1802391	chr5:36958598-37242600	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
22	nsv881136	chr5:36976160-37029885	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3776588	RANBP3L	cis	parietal	SCAN
rs3776588	C5orf42	cis	cerebellum	SCAN
rs3776588	RANBP3L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36940600-36985400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:36948400-36985800	Weak transcription	Colonic Mucosa	Colon
3	chr5:36948600-36996600	Weak transcription	HSMMtube	muscle
4	chr5:36949600-37086800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:36951400-37004400	Weak transcription	Right Ventricle	heart
6	chr5:36952200-36985000	Weak transcription	Small Intestine	intestine
7	chr5:36954400-37026400	Weak transcription	Pancreas	Pancrea
8	chr5:36954800-37023600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:36955400-37010400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:36957600-36985400	Weak transcription	Esophagus	oesophagus
11	chr5:36959400-36988800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:36959400-36996800	Weak transcription	Gastric	stomach
13	chr5:36962400-37028400	Weak transcription	Spleen	Spleen
14	chr5:36964000-36984800	Weak transcription	Ovary	ovary
15	chr5:36965800-37018600	Weak transcription	Psoas Muscle	Psoas
16	chr5:36966000-36998800	Weak transcription	Fetal Heart	heart
17	chr5:36968800-36984800	Weak transcription	Fetal Stomach	stomach
18	chr5:36968800-36996200	Weak transcription	Lung	lung
19	chr5:36968800-37031200	Weak transcription	Aorta	Aorta
20	chr5:36969800-37065000	Weak transcription	Stomach Mucosa	stomach
21	chr5:36972600-37019200	Weak transcription	Brain Angular Gyrus	brain
22	chr5:36974200-36996400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr5:36976400-36984800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:36976400-36984800	Weak transcription	HepG2	liver
25	chr5:36976400-36984800	Weak transcription	HUVEC	blood vessel
26	chr5:36976400-36996200	Weak transcription	Brain Substantia Nigra	brain
27	chr5:36976400-37010600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:36976600-36984800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:36976600-36984800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:36976600-36984800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:36976600-36984800	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:36976600-36984800	Weak transcription	Left Ventricle	heart
33	chr5:36976600-36984800	Weak transcription	K562	blood
34	chr5:36976600-36985200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:36976600-36987400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:36976600-37008800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:36976600-37019200	Weak transcription	NHLF	lung
38	chr5:36976600-37022800	Weak transcription	Fetal Brain Male	brain
39	chr5:36976800-36984800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:36976800-36984800	Weak transcription	Fetal Kidney	kidney
41	chr5:36976800-36985000	Weak transcription	A549	lung
42	chr5:36976800-36988200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr5:36977000-36984600	Weak transcription	HSMM	muscle
44	chr5:36977000-36984800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:36977000-36985200	Weak transcription	Adipose Nuclei	Adipose
46	chr5:36977000-36987400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:36977000-36996000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr5:36977000-37002000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr5:36977000-37003400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr5:36977200-36984600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links