Variant report

Variant	rs6828882
Chromosome Location	chr4:3166196-3166197
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10006373	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012793	1.00[ASN][1000 genomes]
rs10021254	0.83[EUR][1000 genomes]
rs10034669	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10155264	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10488840	0.99[EUR][1000 genomes]
rs16844026	0.99[EUR][1000 genomes]
rs16844028	0.99[EUR][1000 genomes]
rs2003530	0.96[EUR][1000 genomes]
rs2005787	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28436280	0.91[EUR][1000 genomes]
rs28507598	0.81[EUR][1000 genomes]
rs28643391	0.97[EUR][1000 genomes]
rs28834148	1.00[ASN][1000 genomes]
rs3025825	0.97[EUR][1000 genomes]
rs362269	0.80[EUR][1000 genomes]
rs362274	0.95[EUR][1000 genomes]
rs362276	0.90[EUR][1000 genomes]
rs362278	0.99[EUR][1000 genomes]
rs362310	0.83[EUR][1000 genomes]
rs362323	0.97[EUR][1000 genomes]
rs362325	0.80[EUR][1000 genomes]
rs362338	0.99[EUR][1000 genomes]
rs363067	1.00[ASN][1000 genomes]
rs363068	1.00[ASN][1000 genomes]
rs363070	1.00[ASN][1000 genomes]
rs363082	1.00[ASN][1000 genomes]
rs363090	0.92[EUR][1000 genomes]
rs363091	0.92[EUR][1000 genomes]
rs363093	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363094	0.96[EUR][1000 genomes]
rs363095	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs363097	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363098	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363100	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363101	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs363106	0.86[EUR][1000 genomes]
rs363124	0.92[EUR][1000 genomes]
rs363125	0.92[EUR][1000 genomes]
rs363128	0.99[EUR][1000 genomes]
rs363141	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59147561	1.00[ASN][1000 genomes]
rs59588638	0.84[EUR][1000 genomes]
rs61792464	1.00[ASN][1000 genomes]
rs61792535	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6446724	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446725	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828615	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834455	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835567	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839081	0.92[EUR][1000 genomes]
rs6839274	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843895	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7438553	0.95[EUR][1000 genomes]
rs7654034	0.92[EUR][1000 genomes]
rs7663133	1.00[ASN][1000 genomes]
rs7665816	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682324	1.00[ASN][1000 genomes]
rs7683309	0.99[EUR][1000 genomes]
rs7688390	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993781	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3150000-3174400	Weak transcription	HMEC	breast
4	chr4:3156800-3174000	Weak transcription	A549	lung
5	chr4:3158400-3166600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr4:3158600-3173600	Weak transcription	Fetal Kidney	kidney
7	chr4:3159200-3169800	Weak transcription	Stomach Mucosa	stomach
8	chr4:3159400-3173600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:3161000-3169600	Weak transcription	K562	blood
10	chr4:3161200-3169600	Weak transcription	NHDF-Ad	bronchial
11	chr4:3161600-3166800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:3162000-3173800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:3162200-3168000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:3162400-3167800	Weak transcription	Gastric	stomach
15	chr4:3162400-3168000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:3162400-3168000	Weak transcription	Brain Angular Gyrus	brain
17	chr4:3162400-3168000	Weak transcription	Pancreas	Pancrea
18	chr4:3162400-3168000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:3162400-3168200	Weak transcription	Esophagus	oesophagus
20	chr4:3162400-3168200	Weak transcription	Left Ventricle	heart
21	chr4:3162400-3168400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:3162400-3169800	Weak transcription	HSMMtube	muscle
23	chr4:3162400-3173600	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:3162400-3174000	Weak transcription	Brain Substantia Nigra	brain
25	chr4:3162400-3174000	Weak transcription	Ovary	ovary
26	chr4:3162400-3174200	Weak transcription	NHLF	lung
27	chr4:3162400-3174600	Weak transcription	HUVEC	blood vessel
28	chr4:3162400-3175000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:3162600-3167800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:3162600-3167800	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:3162600-3167800	Weak transcription	Fetal Heart	heart
32	chr4:3162600-3168000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:3162600-3168000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:3162600-3168000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:3162600-3168000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:3162600-3168000	Weak transcription	Dnd41	blood
37	chr4:3162600-3168200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:3162600-3168600	Weak transcription	HepG2	liver
39	chr4:3162600-3169600	Weak transcription	NH-A	brain
40	chr4:3162600-3169600	Weak transcription	NHEK	skin
41	chr4:3162600-3169800	Weak transcription	Right Ventricle	heart
42	chr4:3162600-3174000	Weak transcription	Colonic Mucosa	Colon
43	chr4:3162600-3174000	Weak transcription	Hela-S3	cervix
44	chr4:3162600-3174000	Weak transcription	HSMM	muscle
45	chr4:3162600-3182200	Weak transcription	Small Intestine	intestine
46	chr4:3162800-3168000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:3162800-3168000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:3162800-3169600	Weak transcription	GM12878-XiMat	blood
49	chr4:3162800-3169600	Weak transcription	Osteobl	bone
50	chr4:3162800-3174000	Weak transcription	Aorta	Aorta

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