Variant report

Variant	rs2742079
Chromosome Location	chr1:47642230-47642231
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	chr1:47639046..47642799-chr1:47643265..47647842,8	K562	blood:

Variant related genes	Relation type
ENSG00000225506	Chromatin interaction
ENSG00000224805	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10789500	0.81[EUR][1000 genomes]
rs10789501	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10789503	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10890446	0.82[MEX][hapmap]
rs10890457	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs10890460	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs10890464	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs10890468	0.81[EUR][1000 genomes]
rs10890470	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11211446	0.87[CEU][hapmap]
rs11211451	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs11211457	0.87[CEU][hapmap]
rs11211464	0.83[EUR][1000 genomes]
rs11211471	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11211472	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11211475	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12037014	0.86[TSI][hapmap]
rs12734327	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs1847222	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs1847223	0.87[CEU][hapmap]
rs1967757	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2016160	0.87[CEU][hapmap]
rs2208772	0.81[EUR][1000 genomes]
rs2224622	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2494248	0.92[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2798352	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798356	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821082	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28796303	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3850876	0.80[EUR][1000 genomes]
rs4926785	0.87[CEU][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs4926793	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs4926918	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6664392	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs6664496	0.87[CEU][hapmap]
rs6690005	0.87[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs7545034	1.00[CHD][hapmap]
rs7545399	0.83[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs760440	0.84[EUR][1000 genomes]
rs760441	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs760442	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs911903	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs911909	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9793471	0.83[MEX][hapmap];0.82[TSI][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	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2742079	SPATA6	cis	cerebellum	SCAN
rs2742079	HECTD3	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47638800-47644800	Weak transcription	Ovary	ovary
2	chr1:47640000-47644600	Weak transcription	Right Atrium	heart
3	chr1:47640600-47643000	Enhancers	HepG2	liver
4	chr1:47641200-47643800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:47641200-47644200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:47641200-47644200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:47641200-47644200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:47641200-47644400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:47641200-47644400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:47641200-47644400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:47641200-47644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:47641200-47644400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:47641200-47644400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:47641200-47644400	Weak transcription	Osteobl	bone
15	chr1:47641200-47644600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:47641200-47644800	Weak transcription	Liver	Liver
17	chr1:47641200-47644800	Weak transcription	Brain Substantia Nigra	brain
18	chr1:47641400-47644200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:47641400-47644200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:47641400-47644200	Weak transcription	Hela-S3	cervix
21	chr1:47641400-47644200	Weak transcription	HSMM	muscle
22	chr1:47641400-47644400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:47641400-47644400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:47641400-47644400	Weak transcription	Adipose Nuclei	Adipose
25	chr1:47641400-47644400	Weak transcription	Brain Angular Gyrus	brain
26	chr1:47641400-47644400	Weak transcription	Spleen	Spleen
27	chr1:47641400-47644600	Weak transcription	Fetal Kidney	kidney
28	chr1:47641600-47643800	Weak transcription	K562	blood
29	chr1:47641600-47644000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:47641600-47644200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:47641600-47644400	Weak transcription	Brain Anterior Caudate	brain
32	chr1:47641600-47644400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:47641600-47644400	Weak transcription	NHEK	skin
34	chr1:47641600-47644600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:47641600-47645000	Weak transcription	Fetal Lung	lung
36	chr1:47641800-47644200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:47641800-47644400	Weak transcription	HMEC	breast
38	chr1:47641800-47644800	Weak transcription	Brain Hippocampus Middle	brain

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