Variant report

Variant	rs13066914
Chromosome Location	chr3:135738428-135738429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:135738258-135738616	MCF10A-Er-Src	breast:	n/a	n/a
2	FOXA1	chr3:135738428-135738651	T-47D	breast:	n/a	chr3:135738535-135738547

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135716831..135719194-chr3:135738292..135740205,2	MCF-7	breast:
2	chr3:135697805..135699794-chr3:135735661..135738510,2	MCF-7	breast:

Variant related genes	Relation type
PPP2R3A	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13065542	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097248	1.00[ASN][1000 genomes]
rs36060212	1.00[ASN][1000 genomes]
rs67709813	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS 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 target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13066914	MSL2	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135707000-135741600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:135717200-135747000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:135718000-135753000	Weak transcription	Fetal Kidney	kidney
4	chr3:135719000-135741600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:135719200-135746200	Weak transcription	Fetal Intestine Large	intestine
6	chr3:135721800-135763600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:135726200-135748000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:135726400-135758400	Weak transcription	Lung	lung
9	chr3:135727200-135746600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:135727400-135760600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:135727800-135741600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:135727800-135741600	Weak transcription	Pancreas	Pancrea
13	chr3:135727800-135769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:135728000-135748000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:135728200-135746400	Weak transcription	Ovary	ovary
16	chr3:135735600-135741600	Enhancers	Fetal Heart	heart
17	chr3:135735800-135760600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:135736200-135738600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr3:135736400-135738600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr3:135736400-135738600	Enhancers	Stomach Smooth Muscle	stomach
21	chr3:135736400-135738800	Enhancers	Colon Smooth Muscle	Colon
22	chr3:135737000-135740000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:135737200-135738800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:135737200-135739800	Enhancers	NHDF-Ad	bronchial
25	chr3:135737200-135743000	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:135737400-135742200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:135737400-135747200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:135737600-135738600	Enhancers	HSMM	muscle
29	chr3:135737600-135738800	Enhancers	Fetal Lung	lung
30	chr3:135737600-135739000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:135737600-135739600	Enhancers	NHLF	lung
32	chr3:135737600-135740000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:135737600-135741000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:135737800-135738600	Enhancers	Right Ventricle	heart
35	chr3:135737800-135739000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:135737800-135739800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:135737800-135740000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:135738000-135740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:135738000-135741400	Weak transcription	Right Atrium	heart
40	chr3:135738000-135741600	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:135738000-135741600	Weak transcription	Left Ventricle	heart
42	chr3:135738000-135741600	Weak transcription	Psoas Muscle	Psoas
43	chr3:135738000-135745800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:135738000-135750000	Weak transcription	Brain Substantia Nigra	brain
45	chr3:135738000-135758400	Weak transcription	Gastric	stomach
46	chr3:135738000-135761200	Weak transcription	Fetal Brain Male	brain
47	chr3:135738000-135775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:135738200-135738600	Weak transcription	Osteobl	bone
49	chr3:135738200-135739600	Weak transcription	HMEC	breast
50	chr3:135738200-135740800	Weak transcription	NHEK	skin

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