Variant report

Variant	rs312783
Chromosome Location	chr11:68118563-68118564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:68114086..68116989-chr11:68117295..68119405,4	K562	blood:
2	chr11:68113645..68115715-chr11:68116724..68119590,2	MCF-7	breast:
3	chr11:68118415..68120971-chr11:68138628..68140301,2	MCF-7	breast:
4	chr11:68107714..68112282-chr11:68118336..68124263,11	MCF-7	breast:
5	chr11:68116698..68120092-chr11:68121944..68124842,3	MCF-7	breast:
6	chr11:68107929..68111362-chr11:68116810..68118643,3	MCF-7	breast:
7	chr11:68113675..68115970-chr11:68117419..68119405,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11602256	0.86[JPT][hapmap];0.87[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];0.95[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	0.82[AMR][1000 genomes]
rs312778	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.94[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];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs312780	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs312781	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs312782	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312784	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs312785	0.90[AFR][1000 genomes];1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312791	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312792	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]
rs314761	1.00[AFR][1000 genomes];0.98[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];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs314776	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781590	0.86[JPT][hapmap]
rs587808	0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs643892	0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs643981	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659605	0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs671191	0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs74744	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7944040	0.81[CEU][hapmap]
rs91285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv3358277	chr11:68116926-68119724	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs312783	C11orf59	cis	cerebellum	SCAN
rs312783	LTBP3	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68096600-68126000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:68104600-68119600	Enhancers	Liver	Liver
3	chr11:68106200-68121800	Weak transcription	Psoas Muscle	Psoas
4	chr11:68108600-68121800	Weak transcription	HUVEC	blood vessel
5	chr11:68109200-68119800	Weak transcription	Hela-S3	cervix
6	chr11:68110600-68137800	Weak transcription	Brain Angular Gyrus	brain
7	chr11:68110800-68119200	Weak transcription	NH-A	brain
8	chr11:68110800-68125200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:68111000-68122200	Weak transcription	Small Intestine	intestine
10	chr11:68111200-68120400	Weak transcription	HSMM	muscle
11	chr11:68111200-68121600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:68111200-68137400	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:68111400-68121200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:68111400-68126400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:68111600-68121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:68111800-68120600	Weak transcription	NHEK	skin
17	chr11:68111800-68120800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:68112000-68120200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:68112200-68121200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:68113400-68119600	Weak transcription	A549	lung
21	chr11:68113400-68121200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:68113400-68125600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:68113400-68126400	Weak transcription	Fetal Brain Male	brain
24	chr11:68114000-68129600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:68114200-68119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:68114200-68120600	Weak transcription	Osteobl	bone
27	chr11:68114200-68125800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:68114400-68119400	Weak transcription	Fetal Thymus	thymus
29	chr11:68114400-68121000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:68114400-68125400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr11:68114600-68120400	Weak transcription	HMEC	breast
32	chr11:68114800-68118800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:68114800-68119200	Strong transcription	Fetal Stomach	stomach
34	chr11:68114800-68120000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:68114800-68120400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr11:68114800-68120600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:68114800-68138000	Weak transcription	Fetal Kidney	kidney
38	chr11:68115000-68118600	Strong transcription	Dnd41	blood
39	chr11:68115000-68120000	Weak transcription	HSMMtube	muscle
40	chr11:68115000-68126200	Strong transcription	Fetal Intestine Small	intestine
41	chr11:68115200-68119400	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr11:68115200-68126000	Weak transcription	GM12878-XiMat	blood
43	chr11:68115200-68126200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:68115400-68118800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:68115400-68119200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr11:68115400-68120800	Strong transcription	Fetal Intestine Large	intestine
47	chr11:68115400-68120800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:68115400-68135200	Strong transcription	HepG2	liver
49	chr11:68115600-68120000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr11:68115600-68120800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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