Variant report

Variant	rs7618228
Chromosome Location	chr3:52101200-52101201
allele	C/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	MYC	chr3:52101166-52101259	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:52100916-52101452	Hela-S3	cervix:	n/a	n/a
3	EP300	chr3:52101129-52104498	SK-N-SH	brain:	n/a	chr3:52104021-52104037 chr3:52102333-52102347

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52100511..52102649-chr3:52105549..52107890,2	K562	blood:
2	chr3:52099945..52103017-chr3:52111566..52113798,3	K562	blood:

Variant related genes	Relation type
LINC00696	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs6784764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803639	0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7611413	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652969	0.83[AMR][1000 genomes];1.00[EUR][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	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
8	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1836489	chr3:52089837-52101799	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	esv1838771	chr3:52089837-52101799	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52091800-52101800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52091800-52106000	Enhancers	Esophagus	oesophagus
3	chr3:52092000-52102200	Enhancers	HMEC	breast
4	chr3:52092000-52106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:52092200-52101400	Weak transcription	Fetal Intestine Large	intestine
6	chr3:52092200-52102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:52092200-52102800	Weak transcription	Thymus	Thymus
8	chr3:52092200-52104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:52092200-52104800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:52092200-52107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:52092600-52104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:52094000-52102000	Enhancers	NHEK	skin
13	chr3:52096000-52107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52096200-52102000	Enhancers	Fetal Stomach	stomach
15	chr3:52096400-52106400	Weak transcription	Fetal Thymus	thymus
16	chr3:52096800-52104000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:52097000-52102000	Weak transcription	Colonic Mucosa	Colon
18	chr3:52097000-52102000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:52097000-52103600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:52097000-52105000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:52097000-52105000	Weak transcription	Hela-S3	cervix
22	chr3:52097200-52103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:52097200-52104000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:52097400-52101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:52097400-52101800	Weak transcription	NHDF-Ad	bronchial
26	chr3:52097400-52104000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:52097400-52105400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:52097400-52110800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:52097600-52101800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:52097600-52103400	Weak transcription	Brain Substantia Nigra	brain
31	chr3:52097600-52108200	Weak transcription	NHLF	lung
32	chr3:52097600-52119800	Weak transcription	GM12878-XiMat	blood
33	chr3:52098800-52106400	Enhancers	Fetal Muscle Leg	muscle
34	chr3:52099200-52101200	Enhancers	Right Ventricle	heart
35	chr3:52099400-52107000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:52099600-52102600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:52099800-52102000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:52099800-52102000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:52099800-52102200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:52099800-52102800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:52099800-52104600	Weak transcription	HUVEC	blood vessel
42	chr3:52100000-52101200	Weak transcription	Placenta	Placenta
43	chr3:52100000-52102000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:52100000-52102600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:52100000-52103800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:52100000-52104000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:52100000-52104000	Weak transcription	Pancreas	Pancrea
48	chr3:52100000-52104200	Weak transcription	Right Atrium	heart
49	chr3:52100000-52108200	Weak transcription	Gastric	stomach
50	chr3:52100200-52103400	Weak transcription	Monocytes-CD14+_RO01746	blood

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