Variant report

Variant	rs9535181
Chromosome Location	chr13:49839548-49839549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49839099..49842026-chr13:49843722..49845572,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10459375	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459376	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11843587	0.82[EUR][1000 genomes]
rs12385878	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12585196	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]
rs1555672	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs1924659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924661	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038759	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075610	0.84[CHD][hapmap]
rs2147398	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]
rs2181905	0.85[EUR][1000 genomes]
rs2274149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407521	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2407607	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407609	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]
rs3087770	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764131	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]
rs4245351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4941637	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4942809	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942811	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942815	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6561511	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]
rs719614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320595	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320745	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326181	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7326191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328063	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7330892	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7334929	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988621	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7999710	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316437	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316439	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526535	0.86[ASN][1000 genomes]
rs9526537	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526538	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526539	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535173	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535174	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535177	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535182	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535185	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535190	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535192	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535194	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535197	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9535198	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs9535199	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs9562873	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568169	0.84[CHD][hapmap]
rs9568174	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568176	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568179	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568181	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568182	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9591249	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9596077	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596078	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596079	0.81[EUR][1000 genomes]
rs9596080	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[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
rs9535181	LCP1	cis	parietal	SCAN
rs9535181	CAB39L	cis	cerebellum	SCAN
rs9535181	RCBTB1	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49823000-49844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:49823400-49844000	Weak transcription	A549	lung
3	chr13:49823600-49843200	Weak transcription	NHEK	skin
4	chr13:49823800-49855400	Weak transcription	Small Intestine	intestine
5	chr13:49826600-49877800	Weak transcription	Psoas Muscle	Psoas
6	chr13:49831200-49845200	Weak transcription	NH-A	brain
7	chr13:49832000-49843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:49832800-49844800	Strong transcription	Dnd41	blood
9	chr13:49832800-49860600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr13:49832800-49862800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr13:49833000-49865600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr13:49833200-49852600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr13:49833200-49863800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr13:49833200-49866600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:49834000-49846400	Weak transcription	Pancreas	Pancrea
16	chr13:49834200-49855600	Weak transcription	Fetal Intestine Small	intestine
17	chr13:49834200-49875200	Weak transcription	Gastric	stomach
18	chr13:49834600-49845600	Weak transcription	Fetal Kidney	kidney
19	chr13:49834600-49867000	Weak transcription	Thymus	Thymus
20	chr13:49834800-49841400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr13:49834800-49841400	Weak transcription	HUVEC	blood vessel
22	chr13:49834800-49853200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:49834800-49873000	Weak transcription	HMEC	breast
24	chr13:49834800-49875400	Weak transcription	Esophagus	oesophagus
25	chr13:49835200-49843800	Weak transcription	NHLF	lung
26	chr13:49835200-49846800	Weak transcription	HepG2	liver
27	chr13:49835400-49839800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr13:49835400-49862200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:49835600-49841600	Weak transcription	Lung	lung
30	chr13:49835600-49841800	Weak transcription	Osteobl	bone
31	chr13:49835600-49843200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:49835600-49843600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:49835600-49846600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr13:49835600-49846800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:49835600-49866800	Weak transcription	Brain Angular Gyrus	brain
36	chr13:49835600-49866800	Weak transcription	Brain Germinal Matrix	brain
37	chr13:49835600-49867000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:49835600-49867000	Weak transcription	Fetal Brain Male	brain
39	chr13:49835800-49841600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:49835800-49842000	Weak transcription	HSMMtube	muscle
41	chr13:49835800-49845600	Weak transcription	Fetal Heart	heart
42	chr13:49835800-49853000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr13:49835800-49863600	Weak transcription	Right Ventricle	heart
44	chr13:49835800-49875200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr13:49835800-49875200	Weak transcription	GM12878-XiMat	blood
46	chr13:49836000-49840800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:49836000-49851800	Weak transcription	Placenta	Placenta
48	chr13:49836000-49866800	Weak transcription	Colon Smooth Muscle	Colon
49	chr13:49836200-49839800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:49836200-49841800	Weak transcription	HSMM	muscle

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