Variant report

Variant	rs17442142
Chromosome Location	chr7:78307944-78307945
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	chr7:78306457..78309049-chr7:78311061..78313913,2	K562	blood:
2	chr7:78307549..78310108-chr7:78312372..78315266,3	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10228963	1.00[CEU][hapmap]
rs10229438	1.00[CEU][hapmap]
rs10229458	1.00[CEU][hapmap]
rs10230190	1.00[CEU][hapmap]
rs10230478	1.00[CEU][hapmap]
rs10230501	1.00[CEU][hapmap]
rs10243772	1.00[CEU][hapmap]
rs10243883	1.00[CEU][hapmap]
rs10272085	1.00[CEU][hapmap]
rs10273632	1.00[CEU][hapmap]
rs10485909	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs10953681	1.00[CEU][hapmap]
rs10953686	1.00[CEU][hapmap]
rs10953687	1.00[CEU][hapmap]
rs11760430	1.00[CEU][hapmap]
rs11760911	0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs11763541	1.00[CEU][hapmap]
rs11764280	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11768142	1.00[CEU][hapmap]
rs11768372	1.00[CEU][hapmap]
rs11770561	1.00[CEU][hapmap]
rs11770702	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs11773249	1.00[CEU][hapmap]
rs12530747	1.00[CEU][hapmap]
rs12530771	1.00[CEU][hapmap]
rs12530792	1.00[CEU][hapmap]
rs12531353	1.00[CEU][hapmap]
rs12531547	1.00[CEU][hapmap]
rs12531558	1.00[CEU][hapmap]
rs12533182	1.00[CEU][hapmap]
rs12533194	1.00[CEU][hapmap]
rs12533269	1.00[CEU][hapmap]
rs12533873	1.00[CEU][hapmap]
rs12534669	1.00[CEU][hapmap]
rs12534800	1.00[CEU][hapmap]
rs12536628	1.00[CEU][hapmap]
rs12536952	1.00[CEU][hapmap]
rs12536959	1.00[CEU][hapmap]
rs12537842	1.00[CEU][hapmap]
rs12538564	0.87[CEU][hapmap]
rs12538687	1.00[CEU][hapmap]
rs12538706	1.00[CEU][hapmap]
rs12540478	1.00[CEU][hapmap]
rs12540572	1.00[CEU][hapmap]
rs12540597	1.00[CEU][hapmap]
rs12668335	0.85[JPT][hapmap]
rs12669908	0.85[JPT][hapmap]
rs1319590	1.00[ASW][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs13240011	1.00[CEU][hapmap]
rs1496765	1.00[CEU][hapmap]
rs1496774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17151130	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs17151134	0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs17151138	0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs17151148	0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs17151159	1.00[AFR][1000 genomes]
rs17151184	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs17151226	0.85[JPT][hapmap]
rs17151238	0.85[JPT][hapmap]
rs17151281	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs17441871	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1859934	1.00[AFR][1000 genomes]
rs321966	1.00[ASW][hapmap]
rs323132	1.00[AFR][1000 genomes]
rs323141	1.00[AFR][1000 genomes]
rs323142	1.00[AFR][1000 genomes]
rs323143	1.00[AFR][1000 genomes]
rs4370470	1.00[CEU][hapmap]
rs452398	1.00[AFR][1000 genomes]
rs4730412	0.85[JPT][hapmap]
rs4730427	1.00[ASW][hapmap]
rs6953739	1.00[CEU][hapmap]
rs73145155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73145158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73145161	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73145166	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs961659	1.00[ASW][hapmap]

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	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv888509	chr7:78307944-78327299	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17442142	PTHLH	trans	cerebellum	SCAN
rs17442142	L1TD1	trans	lymphoblastoid	seeQTL
rs17442142	PION	cis	cerebellum	SCAN
rs17442142	SGCE	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78301800-78321600	Weak transcription	Fetal Brain Female	brain
2	chr7:78304800-78313000	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:78305400-78312400	Weak transcription	Brain Substantia Nigra	brain
4	chr7:78305400-78312800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:78305800-78308200	Weak transcription	Brain Anterior Caudate	brain
6	chr7:78307200-78309600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:78307400-78308200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr7:78307400-78312600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:78307400-78313600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:78307800-78312800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links