Variant report

Variant	rs10954566
Chromosome Location	chr7:136560407-136560408
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	chr7:136553578..136555415-chr7:136559671..136562489,2	K562	blood:

Variant related genes	Relation type
ENSG00000181072	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10488595	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10488596	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10488597	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10954565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763464	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12530999	1.00[ASN][1000 genomes]
rs12532627	1.00[ASN][1000 genomes]
rs12532672	1.00[ASN][1000 genomes]
rs12533282	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12534748	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12536964	1.00[ASN][1000 genomes]
rs12537069	1.00[ASN][1000 genomes]
rs12537753	1.00[ASN][1000 genomes]
rs12537831	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12538445	1.00[ASN][1000 genomes]
rs12670040	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs13222744	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13223210	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13223738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230245	1.00[ASN][1000 genomes]
rs13233131	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13235508	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13235822	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1424574	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17409631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17409769	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17487790	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17494540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17494589	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17494846	1.00[YRI][hapmap]
rs34166421	1.00[ASN][1000 genomes]
rs34617713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34653588	1.00[ASN][1000 genomes]
rs35641096	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35784011	1.00[ASN][1000 genomes]
rs36007709	1.00[ASN][1000 genomes]
rs62485215	1.00[ASN][1000 genomes]
rs62485218	1.00[ASN][1000 genomes]
rs62485222	1.00[ASN][1000 genomes]
rs62485223	1.00[ASN][1000 genomes]
rs71541328	1.00[ASN][1000 genomes]
rs71541330	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7785651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7811987	1.00[CHB][hapmap];1.00[JPT][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	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10954566	CHRM2	cis	lung	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136557000-136567800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:136557400-136562600	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:136558000-136609200	Weak transcription	Left Ventricle	heart
4	chr7:136558600-136560800	Enhancers	Fetal Heart	heart
5	chr7:136558800-136561400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:136558800-136562800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:136559600-136562400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:136559800-136561400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr7:136560000-136560600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:136560400-136560600	Enhancers	H9 Cell Line	embryonic stem cell
11	chr7:136560400-136560600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr7:136560400-136562200	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links