Variant report

Variant	rs12778288
Chromosome Location	chr10:837153-837154
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:835663..837203-chr10:849697..852402,2	MCF-7	breast:
2	chr10:180500..182203-chr10:836766..839418,2	MCF-7	breast:
3	chr10:829650..833485-chr10:834016..837949,4	MCF-7	breast:
4	chr10:734067..736710-chr10:835595..837174,2	MCF-7	breast:
5	chr10:835224..837627-chr10:1092339..1094785,2	MCF-7	breast:
6	chr10:733781..736812-chr10:835046..837380,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067064	Chromatin interaction
ENSG00000015171	Chromatin interaction
ENSG00000151240	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1555895	0.84[ASN][1000 genomes]
rs4881531	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1050252	chr10:375035-839594	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv540397	chr10:375035-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1048859	chr10:442805-887622	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1039958	chr10:450753-889167	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
7	nsv540400	chr10:450753-889167	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
8	nsv549753	chr10:458477-894838	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1044857	chr10:577396-856059	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv540402	chr10:577396-856059	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv528733	chr10:577444-838378	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1036675	chr10:600206-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
14	nsv948602	chr10:708293-944641	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv949063	chr10:708293-974870	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
17	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
18	nsv1036316	chr10:748848-849979	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv894718	chr10:763714-861390	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv1045119	chr10:766867-855251	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
22	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
23	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
24	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv1048707	chr10:834439-915534	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
26	esv3356062	chr10:835552-839750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv466698	chr10:836115-888073	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
28	nsv549766	chr10:836115-888073	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12778288	LARP5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:831400-850000	Weak transcription	Fetal Heart	heart
2	chr10:835000-841800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr10:835400-838800	Weak transcription	NHDF-Ad	bronchial
4	chr10:835400-843000	Weak transcription	Aorta	Aorta
5	chr10:835600-837400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:835600-837600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:835600-837600	Weak transcription	Fetal Kidney	kidney
8	chr10:835600-838800	Weak transcription	NH-A	brain
9	chr10:835600-841400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:835600-841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr10:835600-842800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:835600-853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:835800-837600	Weak transcription	Fetal Brain Male	brain
14	chr10:835800-838000	Weak transcription	HSMMtube	muscle
15	chr10:835800-838200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:835800-838800	Weak transcription	NHLF	lung
17	chr10:835800-839600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr10:835800-852800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:836000-839200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:836000-840200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr10:836000-841400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:836000-842000	Weak transcription	A549	lung
23	chr10:836000-849000	Weak transcription	Right Ventricle	heart
24	chr10:836000-849400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr10:836000-852000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:836000-852800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr10:836200-837200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:836200-837600	Weak transcription	Pancreas	Pancrea
29	chr10:836200-838000	Weak transcription	Esophagus	oesophagus
30	chr10:836200-838200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:836200-838200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr10:836200-838200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:836200-838200	Weak transcription	HSMM	muscle
34	chr10:836200-840600	Weak transcription	Spleen	Spleen
35	chr10:836200-842800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr10:836200-850200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr10:836200-852000	Weak transcription	Ovary	ovary
38	chr10:836200-852400	Weak transcription	Brain Hippocampus Middle	brain
39	chr10:836200-852600	Weak transcription	Osteobl	bone
40	chr10:836400-837400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:836400-837600	Weak transcription	Gastric	stomach
42	chr10:836400-839000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr10:836400-848600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr10:836400-850400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr10:836600-837400	Weak transcription	Fetal Muscle Leg	muscle
46	chr10:836600-837600	Weak transcription	Lung	lung
47	chr10:836600-853000	Weak transcription	Stomach Mucosa	stomach
48	chr10:837000-838000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr10:837000-838000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr10:837000-842800	Weak transcription	Placenta	Placenta

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