Variant report

Variant	rs4648055
Chromosome Location	chr4:103515313-103515314
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	chr4:103514947..103516619-chr4:103518321..103520402,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1005819	1.00[JPT][hapmap]
rs1020759	0.90[JPT][hapmap]
rs1020760	1.00[JPT][hapmap]
rs11722146	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11723120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs118882	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs12509403	0.84[CEU][hapmap]
rs12509517	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12648696	0.94[CHB][hapmap]
rs1585213	0.91[JPT][hapmap]
rs1585215	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1598859	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs1599961	0.91[JPT][hapmap]
rs1609798	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs17032683	0.85[TSI][hapmap];1.00[YRI][hapmap]
rs17032705	0.91[JPT][hapmap]
rs170731	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1801	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2085549	1.00[YRI][hapmap]
rs2168805	0.86[JPT][hapmap]
rs230491	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230492	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs230493	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap]
rs230495	0.90[JPT][hapmap]
rs230496	0.90[JPT][hapmap]
rs230498	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap]
rs230500	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap]
rs230504	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs230505	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs230509	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230511	0.88[CEU][hapmap]
rs230514	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230515	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs230516	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs230519	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs230520	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs230521	0.91[JPT][hapmap]
rs230525	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs230526	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs230528	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs230529	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs230531	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs230532	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs230533	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230534	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs230535	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs230539	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs230540	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230541	0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs230542	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs2903281	0.85[TSI][hapmap];1.00[YRI][hapmap]
rs3755867	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3774933	0.90[JPT][hapmap]
rs3774936	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3774937	0.84[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs3774938	0.91[JPT][hapmap]
rs3774956	1.00[JPT][hapmap]
rs3774959	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs3774963	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774964	0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs3817685	1.00[JPT][hapmap]
rs3821958	1.00[JPT][hapmap]
rs4235404	0.87[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4456957	1.00[YRI][hapmap]
rs4648011	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs4648058	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4648068	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs4648085	1.00[YRI][hapmap]
rs4648133	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs4698858	1.00[JPT][hapmap]
rs4698861	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs4698863	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4699030	0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs747559	0.91[JPT][hapmap]
rs9790601	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs980455	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4648055	CISD2	cis	parietal	SCAN
rs4648055	ADH7	cis	cerebellum	SCAN
rs4648055	MANBA	cis	multi-tissue	Pritchard
rs4648055	COL9A2	trans	multi-tissue	Pritchard
rs4648055	MANBA	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
2	chr4:103483000-103518600	Weak transcription	Small Intestine	intestine
3	chr4:103483200-103516600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:103483400-103541600	Weak transcription	K562	blood
5	chr4:103488200-103520000	Weak transcription	Fetal Kidney	kidney
6	chr4:103490800-103519200	Weak transcription	Stomach Mucosa	stomach
7	chr4:103495800-103516400	Weak transcription	NHLF	lung
8	chr4:103497000-103516600	Weak transcription	Brain Substantia Nigra	brain
9	chr4:103497600-103533400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr4:103498800-103520600	Weak transcription	Fetal Brain Female	brain
11	chr4:103500200-103515600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:103500200-103527600	Weak transcription	Pancreas	Pancrea
13	chr4:103500400-103516400	Weak transcription	Gastric	stomach
14	chr4:103500400-103522600	Weak transcription	Psoas Muscle	Psoas
15	chr4:103500400-103528200	Weak transcription	Right Ventricle	heart
16	chr4:103500800-103517400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:103502600-103532800	Weak transcription	Brain Germinal Matrix	brain
18	chr4:103502800-103517400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:103503200-103516800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:103504800-103516400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr4:103505000-103517400	Strong transcription	HSMMtube	muscle
22	chr4:103505600-103516600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:103507400-103515800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:103508000-103518600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:103508200-103517400	Weak transcription	Lung	lung
26	chr4:103508200-103518600	Weak transcription	Esophagus	oesophagus
27	chr4:103508200-103522800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:103508400-103515400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr4:103508400-103516800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:103508400-103517400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:103508400-103518600	Weak transcription	Thymus	Thymus
32	chr4:103508400-103519200	Weak transcription	Spleen	Spleen
33	chr4:103508400-103522400	Weak transcription	Fetal Stomach	stomach
34	chr4:103508600-103515600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:103508800-103515400	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:103508800-103518600	Weak transcription	Aorta	Aorta
37	chr4:103509400-103515800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:103509600-103516600	Weak transcription	Hela-S3	cervix
39	chr4:103510200-103515800	Weak transcription	HMEC	breast
40	chr4:103511200-103518600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:103511200-103525000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:103512000-103515400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:103512000-103516000	Weak transcription	Fetal Heart	heart
44	chr4:103512200-103516600	Weak transcription	Colonic Mucosa	Colon
45	chr4:103512400-103515400	Weak transcription	Dnd41	blood
46	chr4:103512400-103515800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:103512400-103516400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:103512400-103521600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:103512600-103515600	Weak transcription	Placenta	Placenta
50	chr4:103512600-103515600	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links