Variant report

Variant	rs62410444
Chromosome Location	chr3:179044310-179044311
allele	A/G
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:5)
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	chr3:179044206-179044402	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:179040612..179043524-chr3:179043815..179047485,6	K562	blood:
2	chr3:179040206..179042939-chr3:179043914..179045418,3	MCF-7	breast:
3	chr3:179039368..179041573-chr3:179044284..179046543,4	MCF-7	breast:
4	chr3:179041141..179044648-chr3:179167085..179169566,4	K562	blood:
5	chr3:179043342..179045158-chr3:179050500..179053191,2	K562	blood:

No data

Variant related genes	Relation type
ZNF639	TF binding region
ENSG00000121864	Chromatin interaction
ENSG00000114450	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1061751	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10937003	0.84[ASN][1000 genomes]
rs11539416	0.84[ASN][1000 genomes]
rs11714246	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714353	0.81[ASN][1000 genomes]
rs11715130	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716462	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720405	0.84[ASN][1000 genomes]
rs12632708	0.85[ASN][1000 genomes]
rs16848314	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3806687	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55916170	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62410442	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410443	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410445	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6794532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73172210	0.83[ASN][1000 genomes]
rs7610174	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642257	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7644501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised 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	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179041800-179046600	Weak transcription	Gastric	stomach
2	chr3:179041800-179046600	Weak transcription	Small Intestine	intestine
3	chr3:179041800-179048000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:179042000-179046200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:179042400-179051800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:179042600-179046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:179042600-179046600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:179042600-179046600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:179042600-179046600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:179042600-179046600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:179042600-179048000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:179042600-179048000	Weak transcription	Colonic Mucosa	Colon
13	chr3:179042600-179054000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:179042800-179044400	Enhancers	HepG2	liver
15	chr3:179042800-179044600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:179042800-179044600	Enhancers	Right Ventricle	heart
17	chr3:179042800-179044800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr3:179042800-179045200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:179042800-179045200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:179042800-179045200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:179042800-179045400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:179042800-179045600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:179042800-179045800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:179042800-179045800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:179042800-179045800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:179042800-179046400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:179042800-179046600	Weak transcription	Brain Angular Gyrus	brain
28	chr3:179042800-179046600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:179042800-179046600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:179042800-179046600	Weak transcription	Thymus	Thymus
31	chr3:179042800-179046600	Weak transcription	HSMMtube	muscle
32	chr3:179042800-179047600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:179043000-179045000	Strong transcription	Fetal Intestine Small	intestine
34	chr3:179043000-179045000	Weak transcription	Fetal Kidney	kidney
35	chr3:179043000-179045600	Weak transcription	Liver	Liver
36	chr3:179043000-179045600	Weak transcription	NHDF-Ad	bronchial
37	chr3:179043000-179045800	Weak transcription	Adipose Nuclei	Adipose
38	chr3:179043000-179046600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:179043000-179046600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:179043000-179046600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:179043000-179046800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:179043000-179046800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:179043000-179048000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:179043000-179048000	Weak transcription	Esophagus	oesophagus
45	chr3:179043000-179050000	Weak transcription	Aorta	Aorta
46	chr3:179043000-179050000	Weak transcription	Psoas Muscle	Psoas
47	chr3:179043000-179054800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:179043000-179054800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:179043000-179055600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:179043200-179044400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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