Variant report

Variant	rs312788
Chromosome Location	chr11:68122295-68122296
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:68114310..68115817-chr11:68120866..68122449,2	MCF-7	breast:
2	chr11:67979553..67982275-chr11:68120280..68122678,2	MCF-7	breast:
3	chr11:68110339..68111126-chr11:68121748..68122498,2	MCF-7	breast:
4	chr11:68122151..68124097-chr11:68131732..68133388,2	MCF-7	breast:
5	chr11:68078248..68080276-chr11:68121608..68123501,2	MCF-7	breast:
6	chr11:68122001..68124063-chr11:68124660..68126260,2	MCF-7	breast:
7	chr11:68107714..68112282-chr11:68118336..68124263,11	MCF-7	breast:
8	chr11:68120512..68122790-chr11:68146125..68148650,2	MCF-7	breast:
9	chr11:68108529..68112071-chr11:68120195..68123404,7	MCF-7	breast:
10	chr11:68038742..68040366-chr11:68121260..68123432,2	MCF-7	breast:
11	chr11:68116698..68120092-chr11:68121944..68124842,3	MCF-7	breast:
12	chr11:68116764..68118383-chr11:68120873..68123073,2	K562	blood:
13	chr11:68096786..68099376-chr11:68121391..68123163,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171067	Chromatin interaction
ENSG00000162337	Chromatin interaction
ENSG00000110066	Chromatin interaction

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]
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];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]
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]
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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs312788	LTBP3	cis	cerebellum	SCAN
rs312788	C11orf59	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68096600-68126000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:68110600-68137800	Weak transcription	Brain Angular Gyrus	brain
3	chr11:68110800-68125200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:68111200-68137400	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:68111400-68126400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:68113400-68125600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:68113400-68126400	Weak transcription	Fetal Brain Male	brain
8	chr11:68114000-68129600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:68114200-68125800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:68114400-68125400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr11:68114800-68138000	Weak transcription	Fetal Kidney	kidney
12	chr11:68115000-68126200	Strong transcription	Fetal Intestine Small	intestine
13	chr11:68115200-68126000	Weak transcription	GM12878-XiMat	blood
14	chr11:68115200-68126200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:68115400-68135200	Strong transcription	HepG2	liver
16	chr11:68115800-68124000	Weak transcription	K562	blood
17	chr11:68116600-68122400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:68116800-68123200	Enhancers	Left Ventricle	heart
19	chr11:68117200-68125200	Weak transcription	Primary T cells from cord blood	blood
20	chr11:68117400-68123200	Enhancers	Rectal Smooth Muscle	rectum
21	chr11:68117400-68125000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:68118600-68123800	Weak transcription	Fetal Lung	lung
23	chr11:68118800-68125000	Weak transcription	Fetal Brain Female	brain
24	chr11:68119200-68123200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:68119200-68123200	Enhancers	Right Ventricle	heart
26	chr11:68119400-68122600	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr11:68119800-68125000	Weak transcription	Fetal Thymus	thymus
28	chr11:68120000-68122600	Enhancers	Pancreas	Pancrea
29	chr11:68120000-68123200	Enhancers	Adipose Nuclei	Adipose
30	chr11:68120200-68123000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:68120200-68123200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:68120200-68123200	Enhancers	Placenta	Placenta
33	chr11:68120200-68123200	Enhancers	Stomach Mucosa	stomach
34	chr11:68120400-68122400	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:68120400-68123200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr11:68120600-68123000	Genic enhancers	Fetal Stomach	stomach
37	chr11:68120600-68123400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:68120800-68122600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr11:68120800-68122800	Enhancers	NHDF-Ad	bronchial
40	chr11:68120800-68123000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:68120800-68123200	Enhancers	Esophagus	oesophagus
42	chr11:68120800-68123200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr11:68121000-68122400	Flanking Active TSS	Osteobl	bone
44	chr11:68121000-68122800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:68121000-68122800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr11:68121000-68123000	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr11:68121000-68123200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:68121000-68123200	Enhancers	Ovary	ovary
49	chr11:68121000-68123400	Enhancers	Fetal Heart	heart
50	chr11:68121000-68123400	Enhancers	NHLF	lung

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