Variant report

Variant	rs38456
Chromosome Location	chr7:30577947-30577948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs2709787	0.82[AMR][1000 genomes]
rs2709790	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28679	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38406	0.82[ASN][1000 genomes]
rs38407	0.88[JPT][hapmap]
rs38408	0.81[ASN][1000 genomes]
rs38409	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs38410	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38411	0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38413	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38414	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38415	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38416	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38417	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38418	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38419	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38420	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38421	0.85[ASN][1000 genomes]
rs38422	0.89[ASN][1000 genomes]
rs38423	0.88[ASN][1000 genomes]
rs38425	0.88[ASN][1000 genomes]
rs38426	0.88[ASN][1000 genomes]
rs38427	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38429	0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs38430	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38432	0.88[ASN][1000 genomes]
rs38433	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38434	0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs38435	0.85[EUR][1000 genomes]
rs38436	0.85[EUR][1000 genomes]
rs38437	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38438	0.89[ASN][1000 genomes]
rs38440	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38441	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs38442	0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38443	0.86[ASN][1000 genomes]
rs38444	0.96[ASN][1000 genomes]
rs38445	0.97[ASN][1000 genomes]
rs38446	0.97[ASN][1000 genomes]
rs38447	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38448	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38450	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38451	0.96[ASN][1000 genomes]
rs38452	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38453	0.99[ASN][1000 genomes]
rs38454	0.99[ASN][1000 genomes]
rs38455	0.96[ASN][1000 genomes]
rs38458	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38459	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs38460	0.99[ASN][1000 genomes]
rs38461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38462	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38463	0.99[ASN][1000 genomes]
rs38464	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38465	0.97[ASN][1000 genomes]
rs38466	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38467	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38468	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38469	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38471	0.89[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs38472	0.94[ASN][1000 genomes]
rs38473	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38478	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38480	0.89[ASN][1000 genomes]
rs38481	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38482	0.87[ASN][1000 genomes]
rs38483	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38485	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs38488	0.83[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs38498	0.84[AMR][1000 genomes]
rs39738	0.89[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs40237	0.88[ASN][1000 genomes]
rs4258	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4259	0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4260	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs973002	0.83[CEU][hapmap];0.89[CHB][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	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv966770	chr7:30562144-30590529	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs38456	AC005154.6	cis	Thyroid	GTEx
rs38456	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38456	AC005154.6	cis	Muscle Skeletal	GTEx
rs38456	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38456	AC005154.8	cis	Thyroid	GTEx
rs38456	AC005154.6	cis	lung	GTEx
rs38456	AC005154.6	cis	Artery Aorta	GTEx
rs38456	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38456	AC005154.6	cis	Stomach	GTEx
rs38456	AC005154.8	cis	Whole Blood	GTEx
rs38456	AC005154.6	cis	Nerve Tibial	GTEx
rs38456	AC005154.8	cis	lung	GTEx
rs38456	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38456	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38456	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38456	AC005154.6	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30545000-30584600	Weak transcription	Aorta	Aorta
2	chr7:30545200-30587600	Weak transcription	HSMMtube	muscle
3	chr7:30545600-30586200	Weak transcription	Brain Anterior Caudate	brain
4	chr7:30554400-30596400	Weak transcription	Fetal Brain Female	brain
5	chr7:30554800-30588600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr7:30555200-30590800	Weak transcription	Spleen	Spleen
7	chr7:30560400-30590800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:30560600-30588200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:30560800-30586400	Weak transcription	Primary B cells from cord blood	blood
10	chr7:30560800-30587600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:30560800-30588400	Weak transcription	Brain Substantia Nigra	brain
12	chr7:30561000-30584600	Weak transcription	Ovary	ovary
13	chr7:30561200-30590400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:30561200-30590600	Weak transcription	Right Ventricle	heart
15	chr7:30561400-30580000	Weak transcription	Esophagus	oesophagus
16	chr7:30561400-30585200	Weak transcription	Fetal Lung	lung
17	chr7:30561600-30586000	Weak transcription	Left Ventricle	heart
18	chr7:30561600-30586000	Weak transcription	Lung	lung
19	chr7:30561600-30586200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:30561600-30590600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:30561600-30606400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:30561800-30585000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:30563000-30599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:30563600-30588800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:30564400-30590600	Weak transcription	Liver	Liver
26	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
27	chr7:30565800-30585000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:30565800-30586200	Weak transcription	Brain Angular Gyrus	brain
29	chr7:30566000-30588600	Weak transcription	Stomach Mucosa	stomach
30	chr7:30568400-30583800	Weak transcription	Fetal Intestine Large	intestine
31	chr7:30569000-30602600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:30570600-30583400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:30571200-30588400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:30572400-30590800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:30573000-30588600	Weak transcription	Psoas Muscle	Psoas
36	chr7:30573000-30590400	Weak transcription	HSMM	muscle
37	chr7:30573000-30590600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr7:30573200-30585800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:30573800-30588400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:30574000-30584400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:30574200-30579400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:30574200-30590600	Weak transcription	GM12878-XiMat	blood
43	chr7:30574800-30587200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:30574800-30601000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:30575000-30585200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:30575000-30588400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:30575200-30588400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr7:30575600-30590600	Weak transcription	Thymus	Thymus
49	chr7:30575600-30600000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr7:30576000-30585000	Weak transcription	Fetal Heart	heart

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