Variant report

Variant	rs72625415
Chromosome Location	chr3:120315001-120315002
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	STAT1	chr3:120314826-120315548	GM12878	blood:	n/a	n/a
2	TAF1	chr3:120314750-120315473	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr3:120314823-120315552	GM10847	blood:	n/a	n/a
4	POLR2A	chr3:120314728-120315679	K562	blood:	n/a	n/a
5	RFX5	chr3:120314734-120315414	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:120314861-120315695	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr3:120314664-120315771	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr3:120314596-120315797	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:120314639-120315740	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr3:120314718-120315760	MCF-7	breast:	n/a	n/a
11	NFIC	chr3:120314948-120315373	HepG2	liver:	n/a	n/a
12	NRF1	chr3:120314777-120315475	H1-hESC	embryonic stem cell:	n/a	chr3:120315232-120315243 chr3:120315174-120315185 chr3:120315119-120315130 chr3:120315174-120315188 chr3:120315020-120315034 chr3:120315023-120315037 chr3:120315119-120315128 chr3:120315025-120315034 chr3:120315119-120315133 chr3:120315023-120315032 chr3:120315171-120315185 chr3:120315174-120315185 chr3:120315023-120315034 chr3:120315116-120315130 chr3:120315174-120315183
13	POLR2A	chr3:120314674-120315512	SK-N-MC	brain:	n/a	n/a
14	FOXP2	chr3:120314805-120315259	SK-N-MC	brain:	n/a	n/a
15	CTCF	chr3:120314962-120315008	MCF-7	breast:	n/a	n/a
16	CHD2	chr3:120314791-120315402	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:120314741-120315709	K562	blood:	n/a	n/a
18	MAZ	chr3:120314606-120315385	HepG2	liver:	n/a	n/a
19	REST	chr3:120314830-120315708	HL-60	blood:	n/a	chr3:120315125-120315145
20	MAZ	chr3:120314804-120315649	Hela-S3	cervix:	n/a	n/a
21	PML	chr3:120314811-120315067	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:120314753-120315785	K562	blood:	n/a	n/a
23	POLR2A	chr3:120314982-120315659	H1-hESC	embryonic stem cell:	n/a	n/a
24	HMGN3	chr3:120314920-120315617	K562	blood:	n/a	n/a
25	ZNF143	chr3:120314660-120315782	K562	blood:	n/a	n/a
26	POLR2A	chr3:120314753-120315872	H1-hESC	embryonic stem cell:	n/a	n/a
27	EGR1	chr3:120314829-120315030	K562	blood:	n/a	chr3:120314970-120314981
28	POLR2A	chr3:120314850-120315640	HepG2	liver:	n/a	n/a
29	STAT3	chr3:120314717-120315210	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:120314612-120315566	PANC-1	pancreas:	n/a	n/a
31	TBP	chr3:120314931-120315627	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:120314735-120315719	GM19193	blood:	n/a	n/a
33	POLR2A	chr3:120314763-120315638	MCF-7	breast:	n/a	n/a
34	RUNX3	chr3:120314682-120315108	GM12878	blood:	n/a	n/a
35	MAZ	chr3:120314592-120315622	GM12878	blood:	n/a	n/a
36	MXI1	chr3:120314771-120315656	HepG2	liver:	n/a	n/a
37	MYC	chr3:120314770-120315671	NB4	blood:	n/a	n/a
38	TAF1	chr3:120314731-120315805	A549	lung:	n/a	n/a
39	POLR2A	chr3:120314864-120315463	HepG2	liver:	n/a	n/a
40	MAX	chr3:120314947-120315503	HepG2	liver:	n/a	n/a
41	STAT3	chr3:120314832-120315543	MCF10A-Er-Src	breast:	n/a	n/a
42	MAX	chr3:120314777-120315366	K562	blood:	n/a	n/a
43	POLR2A	chr3:120314819-120315738	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:120314752-120316829	GM12878	blood:	n/a	n/a
45	YY1	chr3:120314946-120315418	HCT-116	colon:	n/a	n/a
46	POLR2A	chr3:120314720-120315740	GM19099	blood:	n/a	n/a
47	SIN3AK20	chr3:120314891-120315531	PANC-1	pancreas:	n/a	n/a
48	STAT3	chr3:120314879-120315269	MCF10A-Er-Src	breast:	n/a	n/a
49	NRF1	chr3:120314745-120315386	Hela-S3	cervix:	n/a	chr3:120315232-120315243 chr3:120315174-120315185 chr3:120315119-120315130 chr3:120315174-120315188 chr3:120315020-120315034 chr3:120315023-120315037 chr3:120315119-120315128 chr3:120315025-120315034 chr3:120315119-120315133 chr3:120315023-120315032 chr3:120315171-120315185 chr3:120315174-120315185 chr3:120315023-120315034 chr3:120315116-120315130 chr3:120315174-120315183
50	FOS	chr3:120314774-120315123	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:120314958..120315682-chr5:14664161..14664669,2	Hela-S3	cervix:
2	chr3:120313507..120317684-chr3:120458763..120463692,6	MCF-7	breast:
3	chr3:120066931..120069030-chr3:120314504..120317461,2	MCF-7	breast:

Variant related genes	Relation type
NDUFB4	TF binding region
ENSG00000153767	Chromatin interaction
ENSG00000144840	Chromatin interaction
ENSG00000261360	Chromatin interaction
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12635956	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1465837	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1583654	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16831523	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17140281	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17140284	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34438738	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34924588	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35085316	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72625410	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72625411	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72625413	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72625414	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72625416	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7626272	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	esv3427031	chr3:120314687-120317235	Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 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	chr3:120314200-120316000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr3:120314400-120315200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:120314400-120315600	Active TSS	Monocytes-CD14+_RO01746	blood
4	chr3:120314400-120316000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:120314400-120316000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:120314400-120316000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:120314400-120316000	Active TSS	K562	blood
8	chr3:120314400-120316200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:120314400-120317000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr3:120314600-120315200	Active TSS	Brain Germinal Matrix	brain
11	chr3:120314600-120315200	Flanking Active TSS	Fetal Brain Male	brain
12	chr3:120314600-120315200	Active TSS	HepG2	liver
13	chr3:120314600-120315600	Active TSS	Primary monocytes fromperipheralblood	blood
14	chr3:120314600-120315600	Active TSS	Primary B cells from cord blood	blood
15	chr3:120314600-120315800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:120314600-120316000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:120314600-120316000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:120314600-120316000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr3:120314600-120316000	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr3:120314600-120316000	Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr3:120314600-120316000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:120314600-120316000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:120314600-120316000	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr3:120314600-120316000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:120314600-120316000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:120314600-120316000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:120314600-120316000	Active TSS	Liver	Liver
28	chr3:120314600-120316000	Active TSS	Brain Angular Gyrus	brain
29	chr3:120314600-120316000	Active TSS	Brain Anterior Caudate	brain
30	chr3:120314600-120316000	Active TSS	Brain Cingulate Gyrus	brain
31	chr3:120314600-120316000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr3:120314600-120316000	Active TSS	Colonic Mucosa	Colon
33	chr3:120314600-120316000	Active TSS	Colon Smooth Muscle	Colon
34	chr3:120314600-120316000	Active TSS	Fetal Brain Female	brain
35	chr3:120314600-120316000	Active TSS	Fetal Intestine Large	intestine
36	chr3:120314600-120316000	Active TSS	Fetal Intestine Small	intestine
37	chr3:120314600-120316000	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr3:120314600-120316000	Active TSS	Fetal Muscle Leg	muscle
39	chr3:120314600-120316000	Active TSS	Fetal Stomach	stomach
40	chr3:120314600-120316000	Active TSS	Fetal Thymus	thymus
41	chr3:120314600-120316000	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr3:120314600-120316000	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr3:120314600-120316000	Active TSS	Thymus	Thymus
44	chr3:120314600-120316000	Active TSS	HSMM	muscle
45	chr3:120314600-120316000	Active TSS	HSMMtube	muscle
46	chr3:120314600-120316000	Active TSS	HUVEC	blood vessel
47	chr3:120314600-120316000	Active TSS	NHLF	lung
48	chr3:120314600-120316200	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr3:120314600-120316200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:120314600-120316200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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