Variant report

Variant	rs312778
Chromosome Location	chr11:68108332-68108333
allele	C/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:68107593..68111498-chr11:68113363..68117300,5	MCF-7	breast:
2	chr11:67979856..67982977-chr11:68108129..68111573,4	MCF-7	breast:
3	chr11:68037006..68040956-chr11:68105916..68111491,8	MCF-7	breast:
4	chr11:68092547..68094982-chr11:68106128..68108701,3	MCF-7	breast:
5	chr11:68077886..68089318-chr11:68104706..68113920,31	MCF-7	breast:
6	chr11:68092005..68093732-chr11:68106116..68109045,2	K562	blood:
7	chr11:68107714..68112282-chr11:68118336..68124263,11	MCF-7	breast:
8	chr11:68082830..68084506-chr11:68108274..68111199,2	K562	blood:
9	chr11:67980659..67983724-chr11:68104991..68110188,4	MCF-7	breast:
10	chr11:68108161..68113775-chr11:68145002..68152027,11	MCF-7	breast:
11	chr11:68107354..68109500-chr11:68111618..68115254,3	K562	blood:
12	chr11:68106405..68113140-chr11:68145593..68153963,20	MCF-7	breast:
13	chr11:68078044..68085563-chr11:68107392..68113786,23	MCF-7	breast:
14	chr11:68086230..68088365-chr11:68106880..68109067,2	K562	blood:
15	chr11:68107929..68111362-chr11:68116810..68118643,3	MCF-7	breast:

No data

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

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11602256	0.87[MEX][hapmap]
rs160517	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs160607	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178352	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs312779	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312780	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs312781	0.89[CHD][hapmap]
rs312782	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs312783	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]
rs312784	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312785	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs312786	0.89[CHD][hapmap]
rs312788	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]
rs312790	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs312791	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs312792	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]
rs314761	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs314775	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs314776	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs643981	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs659605	0.83[MEX][hapmap]
rs671191	0.83[MEX][hapmap]
rs74744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7944040	0.81[CEU][hapmap]
rs91285	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs312778	PPP6R3	cis	cerebellum	SCAN
rs312778	C11orf59	cis	cerebellum	SCAN
rs312778	LTBP3	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68096600-68109400	Weak transcription	Brain Angular Gyrus	brain
2	chr11:68096600-68126000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:68098000-68109200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:68098400-68115000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:68098600-68108400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:68099000-68109000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:68099200-68108800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:68099800-68108400	Weak transcription	Fetal Kidney	kidney
9	chr11:68099800-68108600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:68100000-68108800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:68100200-68108800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:68100600-68108600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:68101000-68109200	Weak transcription	Small Intestine	intestine
14	chr11:68102600-68110800	Enhancers	Left Ventricle	heart
15	chr11:68103000-68111000	Enhancers	Adipose Nuclei	Adipose
16	chr11:68103800-68109000	Weak transcription	Brain Anterior Caudate	brain
17	chr11:68104400-68109200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:68104400-68110000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:68104600-68110400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr11:68104600-68119600	Enhancers	Liver	Liver
21	chr11:68104800-68108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:68105200-68110200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:68105400-68109600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:68105400-68111000	Enhancers	Fetal Muscle Leg	muscle
25	chr11:68105600-68108800	Weak transcription	Colonic Mucosa	Colon
26	chr11:68105600-68109200	Weak transcription	Fetal Brain Male	brain
27	chr11:68105600-68113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:68105800-68108600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:68105800-68108800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr11:68105800-68109200	Weak transcription	Brain Hippocampus Middle	brain
31	chr11:68106000-68110200	Weak transcription	Fetal Brain Female	brain
32	chr11:68106200-68108400	Weak transcription	Hela-S3	cervix
33	chr11:68106200-68108400	Weak transcription	K562	blood
34	chr11:68106200-68108600	Weak transcription	Placenta	Placenta
35	chr11:68106200-68108800	Weak transcription	Aorta	Aorta
36	chr11:68106200-68108800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:68106200-68109000	Weak transcription	Brain Substantia Nigra	brain
38	chr11:68106200-68109000	Weak transcription	Fetal Stomach	stomach
39	chr11:68106200-68109000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:68106200-68109400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:68106200-68113600	Weak transcription	Spleen	Spleen
42	chr11:68106200-68121800	Weak transcription	Psoas Muscle	Psoas
43	chr11:68106400-68108600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:68106400-68109200	Enhancers	Stomach Smooth Muscle	stomach
45	chr11:68106400-68109800	Weak transcription	HSMMtube	muscle
46	chr11:68106400-68110200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:68106800-68108400	Weak transcription	NHEK	skin
48	chr11:68106800-68109000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:68106800-68109000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr11:68107000-68109000	Enhancers	HepG2	liver

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