Variant report

Variant	rs339703
Chromosome Location	chr3:42726064-42726065
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	JUN	chr3:42724483-42726606	K562	blood:	n/a	chr3:42725654-42725664 chr3:42725654-42725664 chr3:42725572-42725582 chr3:42725572-42725582 chr3:42725656-42725667 chr3:42725572-42725582 chr3:42725573-42725581 chr3:42725655-42725663 chr3:42725654-42725664 chr3:42725572-42725582
2	RCOR1	chr3:42725205-42726613	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42725723..42728637-chr3:42737292..42738802,2	K562	blood:
2	chr3:42724857..42728583-chr3:42742957..42746730,4	K562	blood:
3	chr16:57834269..57835195-chr3:42725633..42726347,2	MCF-7	breast:
4	chr3:42709626..42711413-chr3:42723979..42726333,2	MCF-7	breast:
5	chr3:42720527..42722728-chr3:42723710..42726104,2	MCF-7	breast:

Variant related genes	Relation type
KLHL40	TF binding region
ENSG00000010282	Chromatin interaction
ENSG00000230970	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17030476	0.91[CHB][hapmap]
rs339699	0.86[ASN][1000 genomes]
rs339700	0.86[ASN][1000 genomes]
rs339713	0.85[GIH][hapmap]
rs3890974	0.87[ASN][1000 genomes]
rs3901239	0.85[GIH][hapmap]
rs6805421	0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs72865703	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42724000-42726400	Enhancers	Placenta	Placenta
2	chr3:42724200-42726200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:42724200-42726200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:42724200-42726200	Enhancers	Fetal Muscle Leg	muscle
5	chr3:42724200-42727000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:42724200-42727000	Enhancers	HSMMtube	muscle
7	chr3:42724200-42727400	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:42724200-42727400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr3:42724200-42729400	Enhancers	Fetal Heart	heart
10	chr3:42724400-42726400	Enhancers	Aorta	Aorta
11	chr3:42724400-42726600	Enhancers	Brain Anterior Caudate	brain
12	chr3:42724400-42726800	Enhancers	Brain Angular Gyrus	brain
13	chr3:42724600-42726200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:42724600-42727200	Enhancers	Brain Hippocampus Middle	brain
15	chr3:42724800-42726400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:42724800-42726400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:42724800-42726400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:42724800-42726400	Enhancers	HMEC	breast
19	chr3:42724800-42726400	Enhancers	K562	blood
20	chr3:42724800-42726400	Enhancers	NHDF-Ad	bronchial
21	chr3:42724800-42726400	Enhancers	NHEK	skin
22	chr3:42724800-42726600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:42724800-42727000	Enhancers	HSMM	muscle
24	chr3:42725000-42726200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:42725000-42726200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:42725000-42726400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:42725000-42727000	Enhancers	NHLF	lung
28	chr3:42725200-42726200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:42725200-42726200	Weak transcription	Left Ventricle	heart
30	chr3:42725200-42726200	Weak transcription	Psoas Muscle	Psoas
31	chr3:42725200-42726200	Weak transcription	Right Ventricle	heart
32	chr3:42725200-42726400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:42725200-42726600	Enhancers	Hela-S3	cervix
34	chr3:42725200-42726800	Enhancers	Fetal Muscle Trunk	muscle
35	chr3:42725200-42730000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:42725400-42726200	Weak transcription	Esophagus	oesophagus
37	chr3:42725400-42737000	Weak transcription	Right Atrium	heart
38	chr3:42725600-42726200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:42725800-42726200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr3:42725800-42726200	Enhancers	Osteobl	bone
41	chr3:42725800-42726400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:42725800-42726400	Enhancers	Brain Substantia Nigra	brain
43	chr3:42725800-42726400	Enhancers	Rectal Smooth Muscle	rectum
44	chr3:42725800-42726800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr3:42725800-42727000	Enhancers	Stomach Smooth Muscle	stomach
46	chr3:42726000-42726200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:42726000-42726200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:42726000-42726400	Enhancers	NH-A	brain
49	chr3:42726000-42726600	Enhancers	Colon Smooth Muscle	Colon
50	chr3:42726000-42726600	Enhancers	Rectal Mucosa Donor 29	rectum

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