Variant report

Variant	rs17441871
Chromosome Location	chr7:78301419-78301420
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

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]
rs10953681	1.00[CEU][hapmap]
rs10953686	1.00[CEU][hapmap]
rs10953687	1.00[CEU][hapmap]
rs11760430	1.00[CEU][hapmap]
rs11763541	1.00[CEU][hapmap]
rs11764280	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11768142	1.00[CEU][hapmap]
rs11768372	1.00[CEU][hapmap]
rs11770561	1.00[CEU][hapmap]
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]
rs1319590	0.80[MEX][hapmap]
rs13240011	1.00[CEU][hapmap]
rs1496765	1.00[CEU][hapmap]
rs1496774	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17151281	0.85[JPT][hapmap]
rs17442142	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]
rs4370470	1.00[CEU][hapmap]
rs6953739	1.00[CEU][hapmap]
rs73145155	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73145158	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73145161	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73145166	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv464597	chr7:78269375-78301419	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv607656	chr7:78269375-78301419	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17441871	L1TD1	trans	lymphoblastoid	seeQTL
rs17441871	PTHLH	trans	cerebellum	SCAN
rs17441871	SGCE	trans	lymphoblastoid	seeQTL
rs17441871	PION	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78300800-78301600	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr7:78301000-78305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:78301400-78301800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr7:78301400-78301800	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr7:78301400-78301800	Enhancers	Fetal Brain Female	brain

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