Variant report

Variant	rs2407609
Chromosome Location	chr13:49894824-49894825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49890599..49892411-chr13:49892733..49895453,3	K562	blood:
2	chr13:49888284..49892411-chr13:49892733..49897441,5	K562	blood:
3	chr13:49877297..49879495-chr13:49894000..49896980,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10459375	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10459376	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11838927	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11843587	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12585196	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555672	0.92[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1924659	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1924660	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1924661	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2038759	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075610	0.81[CHD][hapmap]
rs2147398	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2181905	0.86[EUR][1000 genomes]
rs2274149	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2274150	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2407521	0.92[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs2407607	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407608	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3087770	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3764131	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs4245351	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4444233	0.81[CHD][hapmap]
rs4941637	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4942809	0.88[ASN][1000 genomes]
rs4942811	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4942812	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942815	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6561511	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs719614	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7320595	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7320745	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7326181	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7326191	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7328063	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7330892	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7334929	0.88[ASN][1000 genomes]
rs7336018	0.83[GIH][hapmap]
rs7984689	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7985932	0.83[GIH][hapmap]
rs7988621	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7991918	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7992766	0.83[GIH][hapmap]
rs7997545	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7999710	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316434	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs9316437	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316439	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526533	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9526534	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526535	0.82[ASN][1000 genomes]
rs9526537	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526538	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526539	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535173	0.88[ASN][1000 genomes]
rs9535174	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9535177	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535180	0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535181	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs9535182	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535184	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535185	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535190	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535192	0.87[ASN][1000 genomes]
rs9535193	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535194	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535197	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535198	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535199	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535200	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9562873	0.88[ASN][1000 genomes]
rs9568169	0.81[CHD][hapmap]
rs9568176	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568177	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568179	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568181	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568182	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9591249	0.92[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs9596078	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596079	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9596080	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596082	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS 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 target site	42 gene(s)	inside rSNPs	diseases
2	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2407609	RCBTB1	cis	parietal	SCAN
rs2407609	CDADC1	cis	brain	BrainEAC
rs2407609	CAB39L	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49876200-49895000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr13:49876200-49935600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr13:49880600-49896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:49881800-49906800	Weak transcription	Fetal Brain Male	brain
5	chr13:49884600-49895000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr13:49884600-49933600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr13:49884800-49903800	Weak transcription	Fetal Brain Female	brain
8	chr13:49884800-49914200	Weak transcription	Brain Hippocampus Middle	brain
9	chr13:49884800-49925600	Weak transcription	Brain Substantia Nigra	brain
10	chr13:49885000-49895000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:49885600-49933400	Weak transcription	Primary T cells from cord blood	blood
12	chr13:49885800-49926000	Weak transcription	Brain Germinal Matrix	brain
13	chr13:49888400-49903800	Weak transcription	Right Ventricle	heart
14	chr13:49888400-49904000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr13:49888400-49922200	Weak transcription	Gastric	stomach
16	chr13:49888600-49895600	Weak transcription	Esophagus	oesophagus
17	chr13:49888600-49897200	Weak transcription	Fetal Stomach	stomach
18	chr13:49888600-49905600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:49888600-49922200	Weak transcription	Lung	lung
20	chr13:49888800-49895000	Weak transcription	Fetal Intestine Small	intestine
21	chr13:49888800-49903600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr13:49888800-49905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr13:49888800-49908800	Weak transcription	Fetal Intestine Large	intestine
24	chr13:49889000-49896200	Weak transcription	Fetal Heart	heart
25	chr13:49889000-49896800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr13:49889000-49944600	Weak transcription	Brain Angular Gyrus	brain
27	chr13:49889000-49947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr13:49889200-49897200	Weak transcription	Aorta	Aorta
29	chr13:49889200-49900000	Weak transcription	Colonic Mucosa	Colon
30	chr13:49889200-49919400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr13:49889200-49933400	Weak transcription	Brain Anterior Caudate	brain
32	chr13:49889200-49944600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr13:49889600-49900200	Weak transcription	Right Atrium	heart
34	chr13:49889600-49914200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:49889600-49914400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr13:49889600-49914400	Weak transcription	Small Intestine	intestine
37	chr13:49889600-49927400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:49891800-49922000	Weak transcription	Left Ventricle	heart
39	chr13:49893000-49895200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr13:49893200-49895200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:49893400-49895000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr13:49893400-49895000	Enhancers	NHLF	lung
43	chr13:49893400-49895200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr13:49893600-49895800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:49893600-49895800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr13:49893800-49895000	Enhancers	Stomach Smooth Muscle	stomach
47	chr13:49893800-49895800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr13:49894000-49895200	Enhancers	Primary B cells from peripheral blood	blood
49	chr13:49894000-49895800	Enhancers	Ovary	ovary
50	chr13:49894400-49895200	Enhancers	Duodenum Smooth Muscle	Duodenum

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