Variant report

Variant	rs2147398
Chromosome Location	chr13:49884055-49884056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49882439..49884408-chr13:49887006..49888853,2	MCF-7	breast:
2	chr13:49879461..49882243-chr13:49883363..49884932,2	K562	blood:
3	chr13:49874891..49877806-chr13:49883558..49885352,2	K562	blood:
4	chr13:49882177..49886130-chr13:50015699..50019370,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10459375	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459376	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11619804	0.83[CHB][hapmap]
rs11838927	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11843587	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12585196	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]
rs1555672	0.92[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1924659	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1924660	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1924661	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038759	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075610	0.81[CHD][hapmap]
rs2181905	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274149	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407521	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2407607	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2407608	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407609	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]
rs3087770	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764131	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4245351	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4444233	0.81[CHD][hapmap]
rs4941637	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4942809	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942811	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942812	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942815	0.96[CEU][hapmap];0.87[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6561511	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs719614	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7320595	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7320745	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7326181	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7326191	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7328063	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7330892	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7334929	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7336018	0.83[GIH][hapmap]
rs7984689	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7985932	0.83[GIH][hapmap]
rs7988621	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7991918	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7992766	0.83[GIH][hapmap]
rs7997545	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7999710	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316434	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316437	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316439	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526533	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526534	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526535	0.86[ASN][1000 genomes]
rs9526537	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526538	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526539	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535173	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535174	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535177	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535180	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535181	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535182	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535184	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535185	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535190	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535192	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535193	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535194	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535197	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535198	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535199	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535200	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535201	0.86[AFR][1000 genomes]
rs9562873	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568169	0.81[CHD][hapmap]
rs9568174	0.80[EUR][1000 genomes]
rs9568176	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568177	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568179	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568181	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568182	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9591249	1.00[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs9596077	0.88[EUR][1000 genomes]
rs9596078	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596079	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9596080	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3449183	chr13:49882551-49885849	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2147398	CAB39L	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49867200-49884200	Weak transcription	Fetal Brain Female	brain
2	chr13:49875800-49884200	Weak transcription	Primary T cells from cord blood	blood
3	chr13:49875800-49887800	Weak transcription	Fetal Intestine Large	intestine
4	chr13:49875800-49887800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr13:49875800-49891000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr13:49876200-49884200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:49876200-49884200	Weak transcription	Brain Germinal Matrix	brain
8	chr13:49876200-49895000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr13:49876200-49935600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr13:49876400-49887800	Weak transcription	Colonic Mucosa	Colon
11	chr13:49876400-49887800	Weak transcription	Fetal Heart	heart
12	chr13:49876400-49887800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr13:49878200-49893600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr13:49878200-49894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr13:49878400-49888000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr13:49878800-49884200	Weak transcription	Gastric	stomach
17	chr13:49879000-49887800	Weak transcription	Spleen	Spleen
18	chr13:49880200-49885800	Weak transcription	Fetal Kidney	kidney
19	chr13:49880400-49894200	Weak transcription	Primary B cells from cord blood	blood
20	chr13:49880600-49888600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:49880600-49896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr13:49881400-49884600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr13:49881600-49884200	Enhancers	Brain Angular Gyrus	brain
24	chr13:49881600-49884200	Enhancers	Brain Cingulate Gyrus	brain
25	chr13:49881600-49884200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr13:49881600-49884200	Enhancers	Pancreas	Pancrea
27	chr13:49881600-49884800	Enhancers	Brain Substantia Nigra	brain
28	chr13:49881800-49906800	Weak transcription	Fetal Brain Male	brain
29	chr13:49882200-49884200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:49882200-49884600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:49882400-49884200	Weak transcription	HSMMtube	muscle
32	chr13:49882600-49885600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr13:49882800-49884200	Weak transcription	Fetal Thymus	thymus
34	chr13:49882800-49884200	Weak transcription	Lung	lung
35	chr13:49882800-49887800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:49882800-49887800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:49882800-49887800	Weak transcription	Aorta	Aorta
38	chr13:49882800-49887800	Weak transcription	Placenta	Placenta
39	chr13:49882800-49887800	Weak transcription	Right Atrium	heart
40	chr13:49882800-49887800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr13:49882800-49887800	Weak transcription	Stomach Mucosa	stomach
42	chr13:49883000-49884200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr13:49883200-49887600	Weak transcription	NHDF-Ad	bronchial
44	chr13:49883200-49887800	Weak transcription	Liver	Liver
45	chr13:49883400-49884200	Weak transcription	Esophagus	oesophagus
46	chr13:49883400-49884200	Weak transcription	Fetal Lung	lung
47	chr13:49883400-49884400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:49883400-49887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:49883400-49887600	Weak transcription	HepG2	liver
50	chr13:49883400-49887600	Weak transcription	NHEK	skin

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