Variant report

Variant	rs2653817
Chromosome Location	chr3:156547846-156547847
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	chr3:156544049..156546693-chr3:156547441..156549158,2	K562	blood:
2	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11927500	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1430410	0.83[YRI][hapmap]
rs168248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16826858	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16826899	0.87[GIH][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap]
rs16826906	0.87[GIH][hapmap]
rs16826948	0.87[GIH][hapmap]
rs2321395	0.89[ASN][1000 genomes]
rs2633815	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2874490	0.87[GIH][hapmap]
rs2874491	0.87[GIH][hapmap]
rs344071	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs344072	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs344074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344076	0.87[GIH][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes]
rs344078	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs344081	0.97[GIH][hapmap]
rs344083	0.81[AFR][1000 genomes]
rs344085	0.89[GIH][hapmap]
rs344088	0.87[GIH][hapmap]
rs344089	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs344090	0.87[GIH][hapmap]
rs344092	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs414683	0.82[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4441614	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs491423	0.87[GIH][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap]
rs58207863	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6441100	0.93[CEU][hapmap];0.89[GIH][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441103	0.84[GIH][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs6763644	0.87[GIH][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap]
rs6776157	0.83[YRI][hapmap]
rs6787535	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7426821	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7609851	0.87[GIH][hapmap]
rs7618306	0.84[GIH][hapmap]
rs7630909	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7640994	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7641929	0.83[YRI][hapmap]
rs7650127	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9810194	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9820830	0.83[YRI][hapmap]
rs9847692	0.84[GIH][hapmap]
rs9858861	0.83[YRI][hapmap]
rs9861359	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9874866	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2653817	LEKR1	cis	Thyroid	GTEx
rs2653817	LEKR1	cis	cerebellum	SCAN
rs2653817	LEKR1	cis	Heart Left Ventricle	GTEx
rs2653817	LINC00886	cis	Artery Aorta	GTEx
rs2653817	C3orf33	cis	parietal	SCAN
rs2653817	LINC00886	cis	Artery Tibial	GTEx
rs2653817	VEPH1	cis	cerebellum	SCAN
rs2653817	LEKR1	cis	parietal	SCAN
rs2653817	SLC23A3	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156545000-156559600	Weak transcription	Pancreas	Pancrea
2	chr3:156545200-156549800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:156545400-156551000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:156545600-156554000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:156545800-156558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:156546000-156549400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:156546000-156549800	Weak transcription	GM12878-XiMat	blood
8	chr3:156546400-156548000	Weak transcription	K562	blood
9	chr3:156547000-156550200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:156547400-156548400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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