Variant report

Variant	rs11785805
Chromosome Location	chr8:52841870-52841871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52830829..52832627-chr8:52841141..52842793,2	K562	blood:
2	chr8:52810247..52812644-chr8:52840469..52844124,3	K562	blood:

Variant related genes	Relation type
ENSG00000168300	Chromatin interaction
ENSG00000228801	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10087958	0.82[JPT][hapmap]
rs10504130	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs10958300	0.96[ASN][1000 genomes]
rs10958301	0.96[ASN][1000 genomes]
rs10958305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11775587	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11775611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777016	0.96[ASN][1000 genomes]
rs11777714	0.96[ASN][1000 genomes]
rs11778849	0.94[ASN][1000 genomes]
rs11780040	0.96[ASN][1000 genomes]
rs11781330	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs11784869	1.00[ASN][1000 genomes]
rs11787229	0.90[ASN][1000 genomes]
rs12675786	0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs12675907	0.82[ASN][1000 genomes]
rs12676345	0.84[ASN][1000 genomes]
rs12676780	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12676835	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12677407	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12678639	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12679287	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679983	0.83[ASN][1000 genomes]
rs12680128	0.83[ASN][1000 genomes]
rs12681203	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12681734	0.92[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs13265006	0.96[ASN][1000 genomes]
rs13276400	0.84[ASN][1000 genomes]
rs16916820	0.94[ASN][1000 genomes]
rs16916856	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs16916865	0.92[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs16916906	0.96[ASN][1000 genomes]
rs16916961	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17212214	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17212256	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17284746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037138	0.94[ASN][1000 genomes]
rs2037139	0.96[ASN][1000 genomes]
rs2069119	0.84[ASN][1000 genomes]
rs2176120	0.96[ASN][1000 genomes]
rs34058697	0.94[ASN][1000 genomes]
rs34073804	0.85[ASN][1000 genomes]
rs34213209	0.84[ASN][1000 genomes]
rs34319820	0.85[ASN][1000 genomes]
rs34364864	0.94[ASN][1000 genomes]
rs34372756	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34677273	1.00[ASN][1000 genomes]
rs34973406	0.94[ASN][1000 genomes]
rs35032384	1.00[ASN][1000 genomes]
rs35509250	0.84[ASN][1000 genomes]
rs35603537	0.84[ASN][1000 genomes]
rs41453644	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4292674	0.83[ASN][1000 genomes]
rs4321994	0.82[ASN][1000 genomes]
rs4534123	0.83[ASN][1000 genomes]
rs4598243	0.91[ASN][1000 genomes]
rs4626585	0.83[ASN][1000 genomes]
rs57212480	0.94[ASN][1000 genomes]
rs58561048	0.94[ASN][1000 genomes]
rs58583070	0.84[ASN][1000 genomes]
rs59602923	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60153173	0.85[ASN][1000 genomes]
rs60304457	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60796336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61326367	0.84[ASN][1000 genomes]
rs6768	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs6994203	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs71513549	0.83[ASN][1000 genomes]
rs71513552	0.85[ASN][1000 genomes]
rs71513561	0.96[ASN][1000 genomes]
rs71513564	1.00[ASN][1000 genomes]
rs763550	0.94[ASN][1000 genomes]
rs9650179	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650180	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650305	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9792352	0.96[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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11785805	PCMTD1	trans	brain	seeQTL
rs11785805	LOC115294	cis	multi-tissue	Pritchard
rs11785805	PCMTD1	cis	brain	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
2	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
3	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
4	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:52831800-52858400	Weak transcription	Primary T cells from cord blood	blood
6	chr8:52831800-52863400	Weak transcription	Aorta	Aorta
7	chr8:52837800-52851800	Weak transcription	Ovary	ovary
8	chr8:52838000-52853400	Weak transcription	Esophagus	oesophagus
9	chr8:52838800-52842200	Enhancers	Left Ventricle	heart
10	chr8:52840200-52842600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr8:52840800-52842200	Enhancers	Pancreas	Pancrea
12	chr8:52841000-52842200	Enhancers	Right Atrium	heart
13	chr8:52841000-52842400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr8:52841000-52843800	Enhancers	HUVEC	blood vessel
15	chr8:52841400-52842200	Enhancers	Right Ventricle	heart
16	chr8:52841600-52852000	Weak transcription	Lung	lung
17	chr8:52841800-52844600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr8:52841800-52845200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links