Variant report

Variant	rs1417295
Chromosome Location	chr1:85080163-85080164
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85078939..85082218-chr1:85082659..85086975,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf180-1	chr1:85079755-85080350	XLOC_000895
2	lnc-C1orf180-1	chr1:85080035-85080207	XLOC_000895
3	lnc-C1orf180-1	chr1:85080082-85080350	NONHSAT004225

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12119873	0.86[EUR][1000 genomes]
rs12123470	0.84[EUR][1000 genomes]
rs12127160	0.86[EUR][1000 genomes]
rs12137275	0.80[EUR][1000 genomes]
rs12141472	0.82[CEU][hapmap]
rs12145771	0.85[EUR][1000 genomes]
rs1517601	0.87[EUR][1000 genomes]
rs1850508	0.97[ASN][1000 genomes]
rs1850509	0.97[ASN][1000 genomes]
rs1914477	0.86[EUR][1000 genomes]
rs2007454	0.97[ASN][1000 genomes]
rs2203455	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2303307	0.88[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2911591	0.86[EUR][1000 genomes]
rs2911592	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2911594	0.81[EUR][1000 genomes]
rs2911595	0.83[MEX][hapmap]
rs2911597	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2911598	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2911599	1.00[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2911603	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2911604	0.96[ASN][1000 genomes]
rs2911605	0.96[ASN][1000 genomes]
rs2911607	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911609	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2943663	0.96[ASN][1000 genomes]
rs2943671	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2945138	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2945140	0.97[ASN][1000 genomes]
rs2945142	0.96[ASN][1000 genomes]
rs2945143	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2945145	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2945147	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2945153	0.84[EUR][1000 genomes]
rs2994435	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994934	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2994937	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2994938	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2994948	0.82[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2994953	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs2994954	0.86[GIH][hapmap]
rs3021402	0.86[GIH][hapmap]
rs41299545	0.86[EUR][1000 genomes]
rs7517756	0.85[EUR][1000 genomes]
rs880412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1417295	SPATA1	cis	parietal	SCAN
rs1417295	CTBS	cis	multi-tissue	Pritchard
rs1417295	BCL10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85070400-85085200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:85071600-85085000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:85071800-85084800	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:85077200-85085400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:85077800-85082400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:85078000-85084800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:85078200-85080400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:85078200-85081000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:85078400-85085200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:85078600-85082800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:85078600-85085000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:85079000-85085000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:85079400-85080400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:85079400-85080600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:85079600-85080800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:85079800-85080200	ZNF genes & repeats	Pancreas	Pancrea
17	chr1:85080000-85080400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:85080000-85080400	Flanking Active TSS	Colon Smooth Muscle	Colon

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