Variant report

Variant	rs312792
Chromosome Location	chr11:68129679-68129680
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:68108535..68111680-chr11:68129129..68132364,4	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11602256	0.86[JPT][hapmap];0.82[MEX][hapmap]
rs11823032	0.85[JPT][hapmap]
rs160517	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs160607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs178352	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1784237	0.83[AMR][1000 genomes]
rs312778	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs312779	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs312780	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs312781	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs312782	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312783	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];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312784	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs312785	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312786	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs312788	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];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312790	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312791	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs314761	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs314775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs314776	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781590	0.86[JPT][hapmap]
rs587808	0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs643892	0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs643981	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659605	0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs671191	0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs74744	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7944040	0.81[CEU][hapmap]
rs91285	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	esv3347272	chr11:67969427-68218997	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv897857	chr11:68056770-68231240	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv897858	chr11:68077238-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv897859	chr11:68102000-68231240	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv897860	chr11:68102000-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1047532	chr11:68103330-68239242	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv541082	chr11:68103330-68239242	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1039671	chr11:68120571-68206630	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1036561	chr11:68123135-68315685	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv897861	chr11:68129606-68196830	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv897862	chr11:68129606-68236389	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs312792	LTBP3	cis	cerebellum	SCAN
rs312792	C11orf59	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68110600-68137800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:68111200-68137400	Weak transcription	Brain Hippocampus Middle	brain
3	chr11:68114800-68138000	Weak transcription	Fetal Kidney	kidney
4	chr11:68115400-68135200	Strong transcription	HepG2	liver
5	chr11:68121600-68131200	Strong transcription	Fetal Intestine Large	intestine
6	chr11:68121600-68148200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:68121800-68137400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:68121800-68156400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:68122000-68137800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:68122200-68139800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:68122600-68138200	Weak transcription	HUVEC	blood vessel
12	chr11:68122800-68137200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr11:68123200-68132400	Weak transcription	Stomach Mucosa	stomach
14	chr11:68123200-68136800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:68123200-68137000	Weak transcription	Psoas Muscle	Psoas
16	chr11:68123200-68137200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:68123200-68139600	Weak transcription	Brain Substantia Nigra	brain
18	chr11:68123400-68132400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr11:68123400-68136000	Strong transcription	Fetal Muscle Leg	muscle
20	chr11:68124000-68129800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr11:68124000-68137400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr11:68124800-68146600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:68125200-68136000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:68125800-68136000	Strong transcription	Right Ventricle	heart
25	chr11:68126000-68130800	Strong transcription	Adipose Nuclei	Adipose
26	chr11:68126000-68136600	Weak transcription	Right Atrium	heart
27	chr11:68126200-68131800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr11:68126200-68136200	Strong transcription	Liver	Liver
29	chr11:68126200-68136800	Weak transcription	Fetal Heart	heart
30	chr11:68126600-68130800	Strong transcription	Brain Germinal Matrix	brain
31	chr11:68126600-68131600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:68126600-68132400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:68126600-68137200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:68126600-68137600	Weak transcription	NHLF	lung
35	chr11:68126800-68131600	Strong transcription	Fetal Intestine Small	intestine
36	chr11:68126800-68133400	Weak transcription	Small Intestine	intestine
37	chr11:68126800-68135400	Weak transcription	HMEC	breast
38	chr11:68126800-68137400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:68126800-68138200	Weak transcription	HSMM	muscle
40	chr11:68126800-68138200	Weak transcription	NH-A	brain
41	chr11:68127000-68130000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:68127000-68130400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:68127000-68131600	Weak transcription	GM12878-XiMat	blood
44	chr11:68127000-68133600	Weak transcription	Primary T cells from cord blood	blood
45	chr11:68127000-68133600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:68127000-68136600	Weak transcription	K562	blood
47	chr11:68127000-68137200	Weak transcription	Brain Anterior Caudate	brain
48	chr11:68127000-68137600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:68127000-68137800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:68127000-68138000	Weak transcription	Muscle Satellite Cultured Cells	--

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