Variant report

Variant	rs2740544
Chromosome Location	chr13:50617640-50617641
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50610763..50613611-chr13:50614019..50617692,5	K562	blood:
2	chr13:50615806..50618078-chr13:51127045..51129254,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50617572-50618904	ENSG00000231607

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11617754	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs1326120	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2066549	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066557	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2066558	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2066572	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066575	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2066585	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066587	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2066591	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2066594	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2242482	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2687950	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2687951	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2740508	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2740524	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2740545	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760914	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2803839	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2812204	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2812216	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2812217	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2812222	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2997624	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4548769	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4942899	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4942901	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7338055	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs790943	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs7986337	0.83[CHD][hapmap]
rs9535407	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs9568354	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs9568357	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs9568363	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568364	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568366	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs9596215	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9596219	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9596220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv1054415	chr13:50598121-50650938	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1202 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2740544	KCNRG	cis	cerebellum	SCAN
rs2740544	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL
rs2740544	PHF11	cis	cerebellum	SCAN
rs2740544	DLEU2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50578600-50629800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr13:50578800-50654400	Weak transcription	Esophagus	oesophagus
3	chr13:50586800-50654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:50587000-50633800	Weak transcription	Hela-S3	cervix
5	chr13:50587000-50645600	Weak transcription	Spleen	Spleen
6	chr13:50588000-50645600	Weak transcription	Ovary	ovary
7	chr13:50589800-50645600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr13:50590000-50624200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr13:50590200-50653600	Weak transcription	Small Intestine	intestine
10	chr13:50593000-50618600	Weak transcription	HMEC	breast
11	chr13:50594600-50622600	Weak transcription	A549	lung
12	chr13:50594600-50635000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr13:50594800-50641000	Weak transcription	Lung	lung
14	chr13:50594800-50643200	Weak transcription	Brain Hippocampus Middle	brain
15	chr13:50594800-50643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:50595000-50654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr13:50595200-50640000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr13:50595800-50654400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr13:50596400-50620400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:50597000-50624600	Weak transcription	Fetal Lung	lung
21	chr13:50598200-50629800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr13:50598200-50634800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:50598200-50641000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr13:50598600-50626000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr13:50598600-50627800	Weak transcription	Brain Germinal Matrix	brain
26	chr13:50598600-50640000	Weak transcription	Placenta	Placenta
27	chr13:50598600-50650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr13:50601600-50626200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:50601600-50641000	Weak transcription	Left Ventricle	heart
30	chr13:50602000-50618600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr13:50604800-50634000	Weak transcription	NHEK	skin
32	chr13:50605000-50624000	Weak transcription	K562	blood
33	chr13:50606200-50618200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr13:50608600-50621000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr13:50608600-50639800	Weak transcription	NHLF	lung
36	chr13:50610600-50621400	Weak transcription	GM12878-XiMat	blood
37	chr13:50611800-50646400	Strong transcription	Fetal Thymus	thymus
38	chr13:50612200-50639800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr13:50612400-50618600	Strong transcription	Osteobl	bone
40	chr13:50612400-50619800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:50612400-50639800	Strong transcription	Dnd41	blood
42	chr13:50612400-50643000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr13:50612600-50639800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr13:50612600-50644200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr13:50612800-50620400	Weak transcription	Fetal Stomach	stomach
46	chr13:50612800-50622400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:50612800-50645400	Weak transcription	HSMMtube	muscle
48	chr13:50613400-50622600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:50613800-50619400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:50613800-50620400	Weak transcription	Fetal Intestine Small	intestine

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