Variant report

Variant	rs12585196
Chromosome Location	chr13:49886855-49886856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49885803..49888221-chr13:49971631..49973979,2	MCF-7	breast:
2	chr13:49886161..49888656-chr13:49974346..49978416,3	MCF-7	breast:
3	chr13:49879463..49882852-chr13:49885235..49888235,4	MCF-7	breast:
4	chr13:49886834..49889531-chr13:50158388..50161122,2	K562	blood:

Variant related genes	Relation type
ENSG00000102547	Chromatin interaction
ENSG00000136144	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10459375	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10459376	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11619804	0.83[CHB][hapmap]
rs11838927	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11843587	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1555672	0.96[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1924659	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1924660	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1924661	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2038759	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147398	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181905	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2274149	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274150	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2407521	0.96[CEU][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs2407607	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2407608	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2407609	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]
rs3087770	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3764131	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4245351	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4941637	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4942809	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942811	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942812	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942815	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6561511	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs719614	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7320595	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7320745	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7326181	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7326191	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7328063	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7330892	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7334929	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7336018	0.83[GIH][hapmap]
rs7984689	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7985932	0.83[GIH][hapmap]
rs7988621	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7991918	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7992766	0.83[GIH][hapmap]
rs7997545	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7999710	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316434	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316437	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316439	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526533	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526534	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526535	0.84[ASN][1000 genomes]
rs9526537	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526538	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526539	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535173	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535174	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535177	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535180	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535181	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535182	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535184	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535185	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535190	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535192	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535193	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535194	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535197	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535198	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535199	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535200	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9562873	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568176	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568177	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568179	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568181	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568182	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9591249	0.96[CEU][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs9596077	0.85[EUR][1000 genomes]
rs9596078	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9596079	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596080	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12585196	CAB39L	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49875800-49887800	Weak transcription	Fetal Intestine Large	intestine
2	chr13:49875800-49887800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr13:49875800-49891000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:49876200-49895000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr13:49876200-49935600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr13:49876400-49887800	Weak transcription	Colonic Mucosa	Colon
7	chr13:49876400-49887800	Weak transcription	Fetal Heart	heart
8	chr13:49876400-49887800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr13:49878200-49893600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr13:49878200-49894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:49878400-49888000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr13:49879000-49887800	Weak transcription	Spleen	Spleen
13	chr13:49880400-49894200	Weak transcription	Primary B cells from cord blood	blood
14	chr13:49880600-49888600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr13:49880600-49896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr13:49881800-49906800	Weak transcription	Fetal Brain Male	brain
17	chr13:49882800-49887800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:49882800-49887800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr13:49882800-49887800	Weak transcription	Aorta	Aorta
20	chr13:49882800-49887800	Weak transcription	Placenta	Placenta
21	chr13:49882800-49887800	Weak transcription	Right Atrium	heart
22	chr13:49882800-49887800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr13:49882800-49887800	Weak transcription	Stomach Mucosa	stomach
24	chr13:49883200-49887600	Weak transcription	NHDF-Ad	bronchial
25	chr13:49883200-49887800	Weak transcription	Liver	Liver
26	chr13:49883400-49887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:49883400-49887600	Weak transcription	HepG2	liver
28	chr13:49883400-49887600	Weak transcription	NHEK	skin
29	chr13:49883400-49887800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr13:49883400-49887800	Weak transcription	Left Ventricle	heart
31	chr13:49883600-49887600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:49883600-49887600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr13:49883600-49887600	Weak transcription	HMEC	breast
34	chr13:49883600-49887600	Weak transcription	HSMM	muscle
35	chr13:49883600-49887600	Weak transcription	HUVEC	blood vessel
36	chr13:49883600-49887600	Weak transcription	NH-A	brain
37	chr13:49883600-49887600	Weak transcription	Osteobl	bone
38	chr13:49883600-49887800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:49883600-49887800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:49883600-49887800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr13:49883600-49887800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr13:49883600-49887800	Weak transcription	Fetal Muscle Leg	muscle
43	chr13:49883600-49887800	Weak transcription	Ovary	ovary
44	chr13:49883600-49887800	Weak transcription	Psoas Muscle	Psoas
45	chr13:49883600-49887800	Weak transcription	Right Ventricle	heart
46	chr13:49883600-49887800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:49883600-49887800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:49883800-49887600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr13:49883800-49887600	Weak transcription	NHLF	lung
50	chr13:49884000-49887600	Weak transcription	Muscle Satellite Cultured Cells	--

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