Variant report

Variant	rs38437
Chromosome Location	chr7:30559676-30559677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:30553250..30555674-chr7:30559176..30561267,2	MCF-7	breast:
2	chr7:30554900..30557427-chr7:30557872..30559739,2	K562	blood:
3	chr7:30559129..30562106-chr7:30564543..30567467,2	MCF-7	breast:
4	chr7:30557636..30561348-chr7:30563064..30567156,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GARS-8	chr7:30559613-30559993	NONHSAT119871

Variant related genes	Relation type
ENSG00000264520	Chromatin interaction
ENSG00000244480	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs2709787	0.86[EUR][1000 genomes]
rs28679	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38406	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38407	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs38408	0.91[ASN][1000 genomes]
rs38409	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38410	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38411	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38413	0.81[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38414	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38415	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs38416	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38418	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38419	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38421	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38422	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38423	0.99[ASN][1000 genomes]
rs38425	0.99[ASN][1000 genomes]
rs38426	0.99[ASN][1000 genomes]
rs38427	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38428	0.88[ASN][1000 genomes]
rs38429	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38430	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38432	0.99[ASN][1000 genomes]
rs38433	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38434	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38435	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38436	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38438	0.97[ASN][1000 genomes]
rs38440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38441	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs38442	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs38443	0.83[ASN][1000 genomes]
rs38444	0.88[ASN][1000 genomes]
rs38445	0.89[ASN][1000 genomes]
rs38446	0.89[ASN][1000 genomes]
rs38447	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38448	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38450	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38451	0.88[ASN][1000 genomes]
rs38452	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38453	0.88[ASN][1000 genomes]
rs38454	0.88[ASN][1000 genomes]
rs38455	0.86[ASN][1000 genomes]
rs38456	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38458	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38459	0.85[EUR][1000 genomes]
rs38460	0.88[ASN][1000 genomes]
rs38461	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38462	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38463	0.88[ASN][1000 genomes]
rs38464	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38465	0.87[ASN][1000 genomes]
rs38466	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38467	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38468	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38469	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38471	0.83[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs38472	0.84[ASN][1000 genomes]
rs38473	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38474	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38478	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38480	0.82[ASN][1000 genomes]
rs38481	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38483	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38485	0.87[EUR][1000 genomes]
rs38488	0.86[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs38498	0.82[EUR][1000 genomes]
rs39738	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs40237	0.99[ASN][1000 genomes]
rs4258	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4259	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4260	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs973002	0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs38437	AC005154.6	cis	Artery Aorta	GTEx
rs38437	AC005154.6	cis	Muscle Skeletal	GTEx
rs38437	AC005154.6	cis	Artery Tibial	GTEx
rs38437	AC005154.6	cis	lung	GTEx
rs38437	AC005154.6	cis	Heart Left Ventricle	GTEx
rs38437	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38437	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38437	AC005154.6	cis	Stomach	GTEx
rs38437	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38437	AC005154.6	cis	Thyroid	GTEx
rs38437	PRR15	cis	cerebellum	SCAN
rs38437	AC005154.8	cis	Whole Blood	GTEx
rs38437	AC005154.6	cis	Nerve Tibial	GTEx
rs38437	AC005154.8	cis	lung	GTEx
rs38437	AC005154.6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30545000-30584600	Weak transcription	Aorta	Aorta
2	chr7:30545200-30559800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:30545200-30562200	Weak transcription	Small Intestine	intestine
4	chr7:30545200-30587600	Weak transcription	HSMMtube	muscle
5	chr7:30545400-30560200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:30545400-30560600	Weak transcription	Brain Substantia Nigra	brain
7	chr7:30545400-30560600	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:30545400-30576200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:30545400-30576600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:30545600-30586200	Weak transcription	Brain Anterior Caudate	brain
11	chr7:30552200-30559800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:30554000-30577600	Weak transcription	Placenta	Placenta
13	chr7:30554200-30560400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:30554200-30561400	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:30554400-30596400	Weak transcription	Fetal Brain Female	brain
16	chr7:30554600-30574600	Weak transcription	Primary T cells from cord blood	blood
17	chr7:30554800-30588600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:30555200-30590800	Weak transcription	Spleen	Spleen
19	chr7:30556800-30560600	Weak transcription	Fetal Brain Male	brain
20	chr7:30557400-30561200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:30557600-30560000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:30557800-30560600	Weak transcription	Primary B cells from cord blood	blood
23	chr7:30557800-30562600	Enhancers	Fetal Intestine Small	intestine
24	chr7:30558200-30560600	Weak transcription	Colonic Mucosa	Colon
25	chr7:30558200-30568400	Enhancers	Fetal Intestine Large	intestine
26	chr7:30558400-30560000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:30558800-30560400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:30559000-30560000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:30559000-30560000	Weak transcription	NHEK	skin
30	chr7:30559200-30576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:30559400-30559800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:30559400-30560200	Weak transcription	Stomach Mucosa	stomach
33	chr7:30559400-30560600	Weak transcription	Esophagus	oesophagus
34	chr7:30559600-30560200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr7:30559600-30561800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:30559600-30562200	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links