Variant report

Variant	rs7829240
Chromosome Location	chr8:86143794-86143795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86142876..86144930-chr8:86157426..86159475,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185015	Chromatin interaction
ENSG00000258256	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10090196	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10091582	0.82[ASN][1000 genomes]
rs10099251	0.82[ASN][1000 genomes]
rs10106970	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110461	0.82[ASN][1000 genomes]
rs10111971	0.82[ASN][1000 genomes]
rs1021583	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11261469	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11261471	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12541299	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12541445	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12543256	0.90[ASN][1000 genomes]
rs12546106	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12550160	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679400	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13259399	0.81[ASN][1000 genomes]
rs13259464	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1553016	0.82[ASN][1000 genomes]
rs1553017	0.82[ASN][1000 genomes]
rs16913681	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16913721	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17740658	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1845891	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1845892	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1908762	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2006767	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132590	0.89[ASN][1000 genomes]
rs2279700	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279701	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291786	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403083	0.88[ASN][1000 genomes]
rs2403084	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2403085	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2403086	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28374336	0.82[ASN][1000 genomes]
rs28377260	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28439950	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28564613	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28677919	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35558766	0.82[ASN][1000 genomes]
rs3779901	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808538	0.80[ASN][1000 genomes]
rs4150893	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4150897	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4150909	0.86[ASN][1000 genomes]
rs4150944	0.87[ASN][1000 genomes]
rs4150962	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150964	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150974	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150977	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609189	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4617148	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4739698	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4740044	0.80[ASN][1000 genomes]
rs4740045	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4740047	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6605610	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6605611	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6605613	0.82[ASN][1000 genomes]
rs67573812	0.82[ASN][1000 genomes]
rs6987641	0.80[ASN][1000 genomes]
rs6990449	0.82[ASN][1000 genomes]
rs6990452	0.82[ASN][1000 genomes]
rs6993316	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6994113	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7001359	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7004871	0.86[EUR][1000 genomes]
rs7011001	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7821629	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827175	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7839129	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9329908	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv971329	chr8:86094967-86183119	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7829240	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs7829240	LRRCC1	cis	Artery Tibial	GTEx
rs7829240	LRRCC1	cis	Esophagus Mucosa	GTEx
rs7829240	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86133000-86145800	Weak transcription	Gastric	stomach
2	chr8:86133800-86157200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:86134600-86157200	Weak transcription	Right Atrium	heart
4	chr8:86135200-86147000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr8:86135200-86155200	Weak transcription	Primary B cells from cord blood	blood
6	chr8:86135400-86151400	Weak transcription	HepG2	liver
7	chr8:86136000-86157200	Weak transcription	Liver	Liver
8	chr8:86136200-86157000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr8:86136400-86145800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr8:86136400-86157000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr8:86137400-86147000	Weak transcription	Fetal Intestine Large	intestine
12	chr8:86138200-86145800	Weak transcription	Fetal Intestine Small	intestine
13	chr8:86139600-86157200	Weak transcription	Pancreas	Pancrea
14	chr8:86142600-86157200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr8:86143400-86146000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:86143600-86157000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links