Variant report

Variant	rs41272591
Chromosome Location	chr6:30138853-30138854
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30134299..30136514-chr6:30137950..30139841,2	MCF-7	breast:
2	chr6:30127588..30130090-chr6:30135576..30138983,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM40-4	chr6:30138753-30138874	NONHSAT108606

Variant related genes	Relation type
ENSG00000204610	Chromatin interaction
ENSG00000204613	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12175655	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12660499	0.82[EUR][1000 genomes]
rs17188015	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17188113	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17194460	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074477	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239531	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2284167	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2284171	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28730510	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3734837	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815081	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41272587	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56307380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62390201	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62390202	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9348838	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9366753	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9366754	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9368622	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368624	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9378189	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9378221	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391677	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391802	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41272591	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs41272591	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30134600-30139600	Strong transcription	Duodenum Mucosa	Duodenum
2	chr6:30134800-30139600	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr6:30135000-30139000	Strong transcription	Liver	Liver
4	chr6:30135600-30141200	Strong transcription	HepG2	liver
5	chr6:30137200-30139600	Weak transcription	Colonic Mucosa	Colon
6	chr6:30137800-30139400	Strong transcription	Fetal Intestine Small	intestine
7	chr6:30138200-30139000	Strong transcription	Fetal Intestine Large	intestine
8	chr6:30138200-30140200	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links