Variant report

Variant	rs13110866
Chromosome Location	chr4:3340383-3340384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:3340296-3340436	ProgFib	skin:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:3292225..3296816-chr4:3337883..3341063,5	MCF-7	breast:
2	chr4:3338818..3342772-chr4:3461368..3467187,7	MCF-7	breast:
3	chr4:3338889..3343165-chr4:3463099..3467145,4	MCF-7	breast:
4	chr4:3339088..3341066-chr4:3344153..3346803,2	MCF-7	breast:
5	chr4:3330743..3332280-chr4:3339908..3342252,2	MCF-7	breast:
6	chr4:3321816..3324737-chr4:3338680..3341161,2	MCF-7	breast:
7	chr4:3339354..3341969-chr4:3342389..3344050,2	MCF-7	breast:

No data

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000175920	Chromatin interaction
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1120898	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13120043	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126960	1.00[ASN][1000 genomes]
rs13129052	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13130998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133859	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150521	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844124	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16844147	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844152	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844209	0.90[EUR][1000 genomes]
rs34004517	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34052318	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34067673	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34628563	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34780636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34849917	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35150150	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35450001	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35720136	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35825779	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57904538	0.91[ASN][1000 genomes]
rs61211078	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61748736	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608266	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71608267	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71608268	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71608278	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs878004	0.82[ASN][1000 genomes]
rs994425	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs994426	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	13 gene(s)	inside rSNPs	diseases
6	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	esv1803957	chr4:3339038-3343475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv1837613	chr4:3339038-3343475	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:3314400-3348200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:3320000-3344000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:3320400-3351800	Weak transcription	Aorta	Aorta
5	chr4:3321000-3347000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:3323600-3344000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:3323600-3344800	Weak transcription	Fetal Intestine Large	intestine
8	chr4:3324000-3341400	Weak transcription	Esophagus	oesophagus
9	chr4:3324000-3343600	Weak transcription	HSMM	muscle
10	chr4:3324200-3342600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:3324200-3343600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:3325200-3342800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:3325600-3348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:3326200-3341800	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:3326200-3342800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:3326400-3341200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:3326400-3341400	Weak transcription	Brain Angular Gyrus	brain
18	chr4:3326400-3343600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:3326400-3343600	Weak transcription	NHLF	lung
20	chr4:3326400-3343800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:3326400-3344800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:3326400-3348000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:3328400-3343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:3330200-3343600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:3331000-3343600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:3331400-3342400	Weak transcription	Psoas Muscle	Psoas
27	chr4:3332400-3343800	Weak transcription	Fetal Intestine Small	intestine
28	chr4:3332600-3342600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:3332800-3342000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:3332800-3342000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:3332800-3343600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:3332800-3343600	Weak transcription	Primary T cells from cord blood	blood
33	chr4:3332800-3343600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:3333600-3341800	Weak transcription	Gastric	stomach
35	chr4:3334000-3341800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:3334000-3342200	Weak transcription	Pancreas	Pancrea
37	chr4:3334000-3342400	Weak transcription	Left Ventricle	heart
38	chr4:3334000-3345800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
40	chr4:3334400-3341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:3334400-3343600	Weak transcription	Adipose Nuclei	Adipose
42	chr4:3334600-3343600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:3336000-3341000	Enhancers	HUVEC	blood vessel
44	chr4:3337000-3344000	Weak transcription	Fetal Kidney	kidney
45	chr4:3337400-3343600	Weak transcription	Ovary	ovary
46	chr4:3337400-3343600	Weak transcription	Right Ventricle	heart
47	chr4:3337600-3343600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:3338200-3340400	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:3338200-3343600	Weak transcription	Brain Anterior Caudate	brain
50	chr4:3338400-3340800	Weak transcription	Fetal Brain Male	brain

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