Variant report

Variant	rs17079425
Chromosome Location	chr3:47036565-47036566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47036212-47037360	K562	blood:	n/a	n/a
2	POLR2A	chr3:47036291-47040424	K562	blood:	n/a	n/a
3	POLR2A	chr3:47036515-47037261	GM18505	blood:	n/a	n/a
4	POLR2A	chr3:47035944-47039006	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:47036474-47036711	A549	lung:	n/a	n/a
6	POLR2A	chr3:47036236-47038925	K562	blood:	n/a	n/a
7	POLR2A	chr3:47036080-47042185	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:47036354-47038212	A549	lung:	n/a	n/a
9	POLR2A	chr3:47036289-47037836	K562	blood:	n/a	n/a
10	POLR2A	chr3:47035079-47040669	K562	blood:	n/a	n/a
11	POLR2A	chr3:47034482-47040584	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:47036396-47039745	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:47036439-47036624	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:47036411-47036610	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:47036276-47040584	K562	blood:	n/a	n/a
16	POLR2A	chr3:47036329-47040671	HL-60	blood:	n/a	n/a
17	POLR2A	chr3:47036247-47040604	GM12892	blood:	n/a	n/a
18	POLR2A	chr3:47036391-47038903	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47022327..47024798-chr3:47034790..47037154,3	MCF-7	breast:
2	chr3:47029851..47036778-chr3:47036995..47040214,6	MCF-7	breast:

No data

Variant related genes	Relation type
NBEAL2	TF binding region
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12485582	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486248	1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12487863	1.00[JPT][hapmap]
rs12489851	1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12491419	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12493723	1.00[JPT][hapmap]
rs12497141	0.81[AMR][1000 genomes]
rs2305632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305640	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35201996	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3816531	1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683321	1.00[JPT][hapmap]
rs60285825	0.87[AMR][1000 genomes]
rs61364027	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7372834	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638049	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS 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	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
7	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47022400-47039800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:47022400-47041600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:47022400-47041800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:47022400-47042000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
6	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:47023200-47042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:47024400-47039600	Weak transcription	HepG2	liver
9	chr3:47029400-47038200	Strong transcription	Fetal Stomach	stomach
10	chr3:47029600-47038000	Weak transcription	HMEC	breast
11	chr3:47029800-47036600	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:47029800-47038000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:47029800-47038400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:47029800-47039200	Strong transcription	Fetal Intestine Small	intestine
15	chr3:47029800-47040800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:47029800-47040800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:47029800-47041000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:47029800-47042000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:47029800-47042400	Weak transcription	Small Intestine	intestine
20	chr3:47029800-47042600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:47029800-47050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:47030000-47037800	Strong transcription	Fetal Intestine Large	intestine
23	chr3:47030000-47039400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:47030200-47037400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:47030200-47044600	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:47030400-47038200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:47030400-47039600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:47030800-47045600	Weak transcription	Aorta	Aorta
29	chr3:47031000-47036800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:47031000-47038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:47031000-47039600	Weak transcription	A549	lung
32	chr3:47031000-47040000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:47031000-47040400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:47031000-47041800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:47031000-47049600	Strong transcription	Gastric	stomach
36	chr3:47031000-47050200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:47031000-47053000	Strong transcription	Dnd41	blood
38	chr3:47031200-47037400	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr3:47031200-47039800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:47031400-47036600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:47031400-47037400	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr3:47031400-47038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:47031400-47039800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:47031600-47037200	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:47031600-47038000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:47031600-47038000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:47031600-47039800	Strong transcription	Pancreas	Pancrea
48	chr3:47031800-47043400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:47032000-47041800	Weak transcription	HUVEC	blood vessel
50	chr3:47032000-47042400	Strong transcription	Lung	lung

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