Variant report

Variant	rs7997545
Chromosome Location	chr13:49858731-49858732
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	chr13:49857451..49860311-chr13:49862385..49865236,2	MCF-7	breast:
2	chr13:49857967..49860546-chr13:49866178..49867693,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10459375	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10459376	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11838927	0.80[EUR][1000 genomes]
rs11843587	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12385878	0.81[AFR][1000 genomes];0.83[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];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1924661	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2038759	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075610	0.84[CHD][hapmap]
rs2147398	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]
rs2181905	0.93[EUR][1000 genomes];0.81[ASN][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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];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];0.89[EUR][1000 genomes]
rs2407607	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[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];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3087770	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4245351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4941637	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4942809	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942811	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942815	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6561511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs719614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7320595	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320745	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7326181	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7326191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7328063	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7330892	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7334929	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7984689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7988621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7999710	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316439	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526535	0.89[ASN][1000 genomes]
rs9526537	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526538	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526539	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535173	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535174	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535177	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535181	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]
rs9535182	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535185	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535192	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535194	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535197	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535198	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9535199	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9535200	0.81[EUR][1000 genomes]
rs9562873	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568169	0.84[CHD][hapmap]
rs9568174	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9568176	0.94[AFR][1000 genomes];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];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568179	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568181	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568182	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9591249	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs9596077	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9596078	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596079	0.87[EUR][1000 genomes]
rs9596080	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[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
rs7997545	LCP1	cis	parietal	SCAN
rs7997545	CAB39L	cis	cerebellum	SCAN
rs7997545	RCBTB1	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49826600-49877800	Weak transcription	Psoas Muscle	Psoas
2	chr13:49832800-49860600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr13:49832800-49862800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr13:49833000-49865600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr13:49833200-49863800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:49833200-49866600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:49834200-49875200	Weak transcription	Gastric	stomach
8	chr13:49834600-49867000	Weak transcription	Thymus	Thymus
9	chr13:49834800-49873000	Weak transcription	HMEC	breast
10	chr13:49834800-49875400	Weak transcription	Esophagus	oesophagus
11	chr13:49835400-49862200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:49835600-49866800	Weak transcription	Brain Angular Gyrus	brain
13	chr13:49835600-49866800	Weak transcription	Brain Germinal Matrix	brain
14	chr13:49835600-49867000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:49835600-49867000	Weak transcription	Fetal Brain Male	brain
16	chr13:49835800-49863600	Weak transcription	Right Ventricle	heart
17	chr13:49835800-49875200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr13:49835800-49875200	Weak transcription	GM12878-XiMat	blood
19	chr13:49836000-49866800	Weak transcription	Colon Smooth Muscle	Colon
20	chr13:49836200-49866800	Weak transcription	Brain Substantia Nigra	brain
21	chr13:49836600-49866800	Weak transcription	Brain Anterior Caudate	brain
22	chr13:49836600-49867000	Weak transcription	Primary B cells from cord blood	blood
23	chr13:49836600-49867000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr13:49837600-49858800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:49837800-49866600	Weak transcription	Fetal Lung	lung
26	chr13:49838600-49875400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:49842600-49866800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:49842600-49874600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr13:49842800-49866800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:49842800-49869400	Weak transcription	Lung	lung
31	chr13:49842800-49875200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr13:49842800-49875400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:49842800-49875400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr13:49846800-49866800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr13:49848000-49862200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:49848000-49873800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr13:49853000-49865000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:49853200-49867000	Weak transcription	Fetal Thymus	thymus
39	chr13:49853400-49866800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr13:49853800-49866800	Weak transcription	Adipose Nuclei	Adipose
41	chr13:49853800-49867000	Weak transcription	Brain Hippocampus Middle	brain
42	chr13:49853800-49875400	Weak transcription	Primary T cells from cord blood	blood
43	chr13:49853800-49875400	Weak transcription	Fetal Intestine Large	intestine
44	chr13:49854000-49863600	Weak transcription	Aorta	Aorta
45	chr13:49854000-49866800	Weak transcription	Ovary	ovary
46	chr13:49854000-49871400	Weak transcription	Spleen	Spleen
47	chr13:49854000-49875000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:49854000-49875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr13:49854000-49875200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr13:49854000-49877600	Weak transcription	Left Ventricle	heart

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