Variant report

Variant	rs38487
Chromosome Location	chr7:30614508-30614509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:30614064-30615272	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000196295	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1049402	1.00[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1986756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2529437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2709787	0.98[ASN][1000 genomes]
rs2709809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38414	0.81[GIH][hapmap]
rs38416	0.81[GIH][hapmap]
rs38441	0.85[CHB][hapmap]
rs38442	0.84[CHB][hapmap]
rs38450	0.82[CHD][hapmap]
rs38466	0.83[CHB][hapmap]
rs38467	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs38468	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs38469	0.83[CHB][hapmap]
rs38471	0.83[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap]
rs38474	0.82[CHD][hapmap]
rs38478	0.82[CHD][hapmap]
rs38480	0.82[CEU][hapmap]
rs38484	0.82[ASN][1000 genomes]
rs38485	0.96[ASN][1000 genomes]
rs38486	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38488	0.82[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38489	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38493	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38494	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38497	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38498	0.99[ASN][1000 genomes]
rs39738	0.81[CHB][hapmap]
rs4258	0.82[CHB][hapmap]
rs4260	0.81[GIH][hapmap]
rs973002	0.86[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs975537	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1024458	chr7:30601877-30649659	Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3417912	chr7:30612318-30619224	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs38487	AC005154.6	cis	lung	GTEx
rs38487	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38487	AC005154.8	cis	Whole Blood	GTEx
rs38487	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38487	AC005154.6	cis	Stomach	GTEx
rs38487	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38487	AC005154.6	cis	Whole Blood	GTEx
rs38487	AC005154.6	cis	Muscle Skeletal	GTEx
rs38487	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38487	AC005154.6	cis	Nerve Tibial	GTEx
rs38487	CRHR2	cis	parietal	SCAN
rs38487	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38487	AC005154.6	cis	Artery Tibial	GTEx
rs38487	AC005154.6	cis	Artery Aorta	GTEx
rs38487	AC005154.6	cis	Thyroid	GTEx
rs38487	AC005154.6	cis	Heart Left Ventricle	GTEx
rs38487	LOC222159	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
2	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
3	chr7:30597400-30633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:30597600-30624400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:30598400-30623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:30599400-30617400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:30601800-30633000	Weak transcription	Hela-S3	cervix
8	chr7:30602800-30615400	Weak transcription	Fetal Brain Female	brain
9	chr7:30602800-30616200	Weak transcription	Fetal Brain Male	brain
10	chr7:30603200-30621000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr7:30603200-30628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:30604000-30615000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:30604000-30615200	Weak transcription	HepG2	liver
14	chr7:30604000-30615200	Weak transcription	NHEK	skin
15	chr7:30604000-30615400	Weak transcription	NHDF-Ad	bronchial
16	chr7:30604600-30617800	Weak transcription	Right Ventricle	heart
17	chr7:30604600-30624400	Weak transcription	Gastric	stomach
18	chr7:30605600-30628200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:30607000-30617400	Weak transcription	Esophagus	oesophagus
20	chr7:30607000-30617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:30607000-30633400	Weak transcription	Fetal Kidney	kidney
22	chr7:30607600-30617400	Weak transcription	Brain Angular Gyrus	brain
23	chr7:30608200-30617400	Weak transcription	NHLF	lung
24	chr7:30608200-30618400	Weak transcription	Brain Substantia Nigra	brain
25	chr7:30608400-30615600	Weak transcription	Fetal Lung	lung
26	chr7:30608400-30616600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:30608400-30617400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:30608400-30617400	Weak transcription	Pancreas	Pancrea
29	chr7:30608400-30617400	Weak transcription	Spleen	Spleen
30	chr7:30608400-30617600	Weak transcription	Brain Anterior Caudate	brain
31	chr7:30608600-30617400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:30608600-30618000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:30609800-30614600	Strong transcription	Liver	Liver
34	chr7:30609800-30621400	Weak transcription	K562	blood
35	chr7:30610200-30614800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:30610400-30616200	Weak transcription	HSMM	muscle
37	chr7:30610400-30617400	Weak transcription	Lung	lung
38	chr7:30610400-30617400	Weak transcription	Thymus	Thymus
39	chr7:30610600-30617400	Weak transcription	Fetal Intestine Small	intestine
40	chr7:30610600-30617400	Weak transcription	Small Intestine	intestine
41	chr7:30610600-30617400	Weak transcription	NH-A	brain
42	chr7:30612000-30614600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:30612000-30614600	Strong transcription	Brain Hippocampus Middle	brain
44	chr7:30612000-30614600	Strong transcription	HSMMtube	muscle
45	chr7:30612000-30614800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
46	chr7:30612000-30614800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr7:30612000-30614800	Strong transcription	Fetal Muscle Leg	muscle
48	chr7:30612000-30615000	Strong transcription	Adipose Nuclei	Adipose
49	chr7:30612000-30615000	Strong transcription	Fetal Stomach	stomach
50	chr7:30612000-30615800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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