Variant report

Variant	rs72625416
Chromosome Location	chr3:120319702-120319703
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	POLR2A	chr3:120319629-120319973	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:120317106-120323167	K562	blood:	n/a	n/a
3	MXI1	chr3:120319342-120321504	SK-N-SH	brain:	n/a	n/a
4	STAT3	chr3:120319615-120319720	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:120319453-120320127	GM12878	blood:	n/a	n/a
6	EP300	chr3:120317993-120322832	SK-N-SH	brain:	n/a	chr3:120319021-120319029

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120319088..120321707-chr3:120460414..120462784,2	MCF-7	breast:

Variant related genes	Relation type
NDUFB4	TF binding region
ENSG00000144840	Chromatin interaction
ENSG00000153767	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12635956	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1465837	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1583654	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831523	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17140281	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17140284	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34438738	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34924588	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35085316	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72625410	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72625411	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625413	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625414	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625415	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7626272	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs805015	0.80[AMR][1000 genomes]
rs805016	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv508238	chr3:120248574-120329424	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120315800-120320200	Weak transcription	Pancreas	Pancrea
2	chr3:120315800-120323600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:120315800-120337200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:120316200-120323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:120316200-120323800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:120316200-120335200	Weak transcription	Esophagus	oesophagus
7	chr3:120316400-120319800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:120316400-120320000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:120316600-120321800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:120316600-120322200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:120316600-120322200	Strong transcription	HSMM	muscle
12	chr3:120316600-120322400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:120316600-120323600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:120316800-120319800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:120316800-120319800	Strong transcription	NHDF-Ad	bronchial
16	chr3:120316800-120320600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:120316800-120320800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:120316800-120321800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:120316800-120321800	Strong transcription	Placenta	Placenta
20	chr3:120316800-120322000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:120316800-120322000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:120316800-120322000	Strong transcription	HMEC	breast
23	chr3:120316800-120322000	Strong transcription	NH-A	brain
24	chr3:120316800-120322200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr3:120316800-120322200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:120316800-120322200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:120316800-120322200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:120316800-120322400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:120316800-120322600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:120316800-120322600	Strong transcription	Fetal Thymus	thymus
31	chr3:120316800-120323400	Weak transcription	Colonic Mucosa	Colon
32	chr3:120317000-120322400	Strong transcription	Primary B cells from cord blood	blood
33	chr3:120317000-120322800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:120317200-120320200	Weak transcription	Gastric	stomach
35	chr3:120317200-120322000	Strong transcription	Osteobl	bone
36	chr3:120317200-120322400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:120317600-120320400	Weak transcription	NHEK	skin
38	chr3:120317600-120321000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:120317600-120322600	Strong transcription	Fetal Intestine Large	intestine
40	chr3:120317800-120320000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:120317800-120320000	Weak transcription	Aorta	Aorta
42	chr3:120317800-120320400	Weak transcription	Spleen	Spleen
43	chr3:120317800-120321000	Weak transcription	Lung	lung
44	chr3:120317800-120322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:120317800-120323200	Weak transcription	Right Atrium	heart
46	chr3:120317800-120323600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:120318000-120320000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:120318000-120320400	Weak transcription	Brain Germinal Matrix	brain
49	chr3:120318000-120322400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr3:120318200-120320200	Enhancers	Brain Anterior Caudate	brain

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