Variant report

Variant	rs7688390
Chromosome Location	chr4:3098889-3098890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3097049..3099921-chr4:3101807..3103894,2	K562	blood:
2	chr4:3093596..3096340-chr4:3097378..3100304,2	K562	blood:
3	chr4:3098722..3101288-chr4:3104828..3107069,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10006373	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012793	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021254	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs10034669	0.85[EUR][1000 genomes]
rs10155264	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10488840	0.85[EUR][1000 genomes]
rs110501	0.83[LWK][hapmap]
rs16844026	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs16844028	0.85[EUR][1000 genomes]
rs17780797	0.94[AFR][1000 genomes]
rs2003530	0.82[EUR][1000 genomes]
rs2005787	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071655	0.83[ASW][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs2285086	0.83[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs28436280	0.90[EUR][1000 genomes]
rs28643391	0.86[EUR][1000 genomes]
rs28834148	1.00[ASN][1000 genomes]
rs28867436	0.92[AFR][1000 genomes]
rs3025825	0.83[EUR][1000 genomes]
rs362274	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs362276	0.89[EUR][1000 genomes]
rs362278	0.85[EUR][1000 genomes]
rs362303	0.85[CEU][hapmap]
rs362310	1.00[CEU][hapmap]
rs362323	0.83[EUR][1000 genomes]
rs362325	0.84[CEU][hapmap]
rs362331	0.98[LWK][hapmap];0.85[YRI][hapmap]
rs362338	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs363063	0.86[AFR][1000 genomes]
rs363067	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363068	1.00[ASN][1000 genomes]
rs363070	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363082	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363090	0.91[EUR][1000 genomes]
rs363091	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes]
rs363093	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363094	0.82[EUR][1000 genomes]
rs363095	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs363097	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363098	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363100	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363101	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs363106	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs363124	0.91[EUR][1000 genomes]
rs363125	0.91[EUR][1000 genomes]
rs363128	0.85[EUR][1000 genomes]
rs363141	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690072	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs4690073	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs59147561	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792464	1.00[ASN][1000 genomes]
rs61792535	0.90[EUR][1000 genomes]
rs6446723	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs6446724	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446725	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828615	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828882	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829069	1.00[CHD][hapmap]
rs6834455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835567	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839081	0.91[EUR][1000 genomes]
rs6839274	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844859	0.85[YRI][hapmap]
rs7438553	0.81[EUR][1000 genomes]
rs7654034	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7663133	1.00[ASN][1000 genomes]
rs7665816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667354	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682324	1.00[ASN][1000 genomes]
rs7683309	0.85[EUR][1000 genomes]
rs7691627	0.83[ASW][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs82333	0.83[LWK][hapmap]
rs916171	0.98[LWK][hapmap];0.89[YRI][hapmap]
rs9993542	1.00[CHD][hapmap]
rs9993781	0.85[EUR][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7688390	TMEM129	cis	parietal	SCAN
rs7688390	OTOP1	cis	cerebellum	SCAN
rs7688390	SH3BP2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3078000-3101000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:3078000-3103000	Weak transcription	Colonic Mucosa	Colon
3	chr4:3078200-3101000	Weak transcription	Brain Substantia Nigra	brain
4	chr4:3078200-3109800	Weak transcription	Stomach Mucosa	stomach
5	chr4:3078400-3102200	Weak transcription	Hela-S3	cervix
6	chr4:3078400-3107000	Weak transcription	HMEC	breast
7	chr4:3078600-3101000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:3078600-3113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:3078800-3108800	Weak transcription	Psoas Muscle	Psoas
10	chr4:3079800-3107200	Weak transcription	Fetal Brain Male	brain
11	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
12	chr4:3081600-3101000	Weak transcription	Spleen	Spleen
13	chr4:3081800-3101600	Weak transcription	Ovary	ovary
14	chr4:3081800-3101600	Weak transcription	Right Ventricle	heart
15	chr4:3084400-3109000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:3084600-3102000	Weak transcription	Gastric	stomach
17	chr4:3084600-3109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:3085600-3107000	Weak transcription	K562	blood
19	chr4:3087200-3101000	Weak transcription	Pancreas	Pancrea
20	chr4:3087400-3101800	Weak transcription	NHEK	skin
21	chr4:3087800-3108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:3089400-3101600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:3089600-3100800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:3090000-3100800	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:3090600-3101200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:3090600-3101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:3091000-3099800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:3091000-3100800	Weak transcription	HUVEC	blood vessel
30	chr4:3091000-3101000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:3091000-3101600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:3092400-3101800	Weak transcription	NH-A	brain
33	chr4:3092400-3108200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr4:3093000-3101600	Weak transcription	NHLF	lung
35	chr4:3093400-3108800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:3093600-3109200	Weak transcription	Fetal Heart	heart
37	chr4:3094400-3123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:3094600-3099000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr4:3094600-3105000	Strong transcription	Primary B cells from cord blood	blood
40	chr4:3094800-3101600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:3095000-3100000	Weak transcription	Brain Angular Gyrus	brain
42	chr4:3095000-3100800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:3095000-3101000	Weak transcription	Fetal Intestine Small	intestine
44	chr4:3095000-3108200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:3095200-3100400	Weak transcription	Brain Germinal Matrix	brain
46	chr4:3095200-3101000	Weak transcription	Fetal Thymus	thymus
47	chr4:3095200-3101200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:3095200-3109000	Weak transcription	A549	lung
49	chr4:3095400-3100800	Weak transcription	Fetal Lung	lung
50	chr4:3095400-3100800	Weak transcription	HSMM	muscle

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