Variant report

Variant	rs3764131
Chromosome Location	chr13:49823287-49823288
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49547950..49551813-chr13:49821954..49825536,3	K562	blood:
2	chr13:49820702..49823407-chr13:50017509..50020339,3	MCF-7	breast:
3	chr13:49813281..49816019-chr13:49822411..49824053,2	K562	blood:

Variant related genes	Relation type
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction
ENSG00000102531	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10459375	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459376	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11843587	0.81[EUR][1000 genomes]
rs12385878	0.82[EUR][1000 genomes]
rs12585196	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]
rs1555672	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs1924659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924661	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038759	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2147398	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]
rs2181905	0.87[EUR][1000 genomes]
rs2274149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407521	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2407607	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407609	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]
rs3087770	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4245351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4941637	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs4942809	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942811	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942815	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6561511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320595	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320745	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326181	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7326191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328063	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7330892	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7334929	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988621	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7999710	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316437	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316439	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526535	0.86[ASN][1000 genomes]
rs9526537	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526538	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526539	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535173	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535174	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535177	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535182	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535185	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535190	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535192	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535193	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535194	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535197	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs9535198	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9535199	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9562873	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568174	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568176	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568179	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568181	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568182	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9591249	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9596077	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596078	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596079	0.82[EUR][1000 genomes]
rs9596080	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[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
rs3764131	CAB39L	cis	cerebellum	SCAN
rs3764131	LCP1	cis	parietal	SCAN
rs3764131	RCBTB1	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49821000-49823400	Active TSS	K562	blood
2	chr13:49821200-49823400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr13:49821200-49823400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr13:49821200-49823400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr13:49821200-49823400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr13:49821400-49823400	Active TSS	NHDF-Ad	bronchial
7	chr13:49821400-49823400	Active TSS	NHLF	lung
8	chr13:49821600-49823400	Active TSS	Brain Anterior Caudate	brain
9	chr13:49821600-49823400	Active TSS	A549	lung
10	chr13:49821600-49823600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:49821800-49823400	Active TSS	NHEK	skin
12	chr13:49822600-49823400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr13:49822600-49823400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr13:49822600-49823400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:49822600-49823400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr13:49822600-49823400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr13:49822600-49823600	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr13:49822600-49823800	Flanking Active TSS	Dnd41	blood
19	chr13:49822600-49824200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr13:49822600-49824800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr13:49822600-49826200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr13:49822800-49823400	Flanking Active TSS	Osteobl	bone
23	chr13:49823000-49823400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr13:49823000-49823400	Enhancers	Brain Substantia Nigra	brain
25	chr13:49823000-49823400	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr13:49823000-49823400	Active TSS	HepG2	liver
27	chr13:49823000-49823600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr13:49823000-49823600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr13:49823000-49823600	Enhancers	Brain Angular Gyrus	brain
30	chr13:49823000-49823800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr13:49823000-49823800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr13:49823000-49824000	Enhancers	Fetal Heart	heart
33	chr13:49823000-49824800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:49823000-49826200	Weak transcription	Gastric	stomach
35	chr13:49823000-49826200	Weak transcription	Pancreas	Pancrea
36	chr13:49823000-49826200	Weak transcription	Psoas Muscle	Psoas
37	chr13:49823000-49826200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr13:49823000-49826200	Weak transcription	Spleen	Spleen
39	chr13:49823000-49826600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr13:49823000-49827800	Weak transcription	Aorta	Aorta
41	chr13:49823000-49828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr13:49823000-49829200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:49823000-49829200	Weak transcription	HSMMtube	muscle
44	chr13:49823000-49833600	Weak transcription	Esophagus	oesophagus
45	chr13:49823000-49833600	Weak transcription	Lung	lung
46	chr13:49823000-49833600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr13:49823000-49833800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr13:49823000-49833800	Weak transcription	Fetal Brain Male	brain
49	chr13:49823000-49836400	Weak transcription	Colonic Mucosa	Colon
50	chr13:49823000-49837000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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