Variant report

Variant	rs62567919
Chromosome Location	chr9:79008644-79008645
allele	G/T
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	E2F6	chr9:79008627-79009718	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:79008625-79010078	Gliobla	brain:	n/a	n/a
3	TBP	chr9:79008578-79010208	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:79008547-79010015	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:79008482-79010203	Hela-S3	cervix:	n/a	n/a
6	TBL1XR1	chr9:79008560-79009977	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:79008604-79010206	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr9:79008420-79010195	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr9:79008577-79009000	GM12891	blood:	n/a	n/a
10	RELA	chr9:79008531-79010131	GM12892	blood:	n/a	chr9:79009597-79009606 chr9:79009597-79009606
11	POLR2A	chr9:79008567-79010148	MCF-7	breast:	n/a	n/a
12	CEBPB	chr9:79008389-79008906	GM12878	blood:	n/a	chr9:79008596-79008609 chr9:79008598-79008609 chr9:79008593-79008610
13	MAX	chr9:79008403-79010324	A549	lung:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
14	USF1	chr9:79008639-79009502	ECC-1	luminal epithelium:	n/a	chr9:79008940-79008956
15	MYC	chr9:79008622-79008948	MCF-7	breast:	n/a	chr9:79008915-79008924
16	BHLHE40	chr9:79008570-79009868	GM12878	blood:	n/a	chr9:79008940-79008956
17	POLR2A	chr9:79008640-79009636	HepG2	liver:	n/a	n/a
18	RCOR1	chr9:79008427-79010596	K562	blood:	n/a	n/a
19	BCL11A	chr9:79008599-79008848	GM12878	blood:	n/a	n/a
20	RELA	chr9:79008558-79009989	GM15510	blood:	n/a	chr9:79009597-79009606 chr9:79009597-79009606
21	POLR2A	chr9:79008608-79009633	A549	lung:	n/a	n/a
22	TFAP2C	chr9:79008581-79010215	Hela-S3	cervix:	n/a	chr9:79009528-79009543
23	USF2	chr9:79008644-79009264	GM12878	blood:	n/a	chr9:79008961-79008972 chr9:79008940-79008956
24	USF2	chr9:79008617-79009229	Hela-S3	cervix:	n/a	chr9:79008961-79008972 chr9:79008940-79008956
25	TAF1	chr9:79008623-79009612	HepG2	liver:	n/a	n/a
26	YY1	chr9:79008588-79009047	GM12892	blood:	n/a	n/a
27	WRNIP1	chr9:79008583-79008924	GM12878	blood:	n/a	n/a
28	MAX	chr9:79008627-79010219	NB4	blood:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
29	MAX	chr9:79008482-79009989	HCT-116	colon:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
30	POLR2A	chr9:79008504-79009429	GM12878	blood:	n/a	n/a
31	BCL3	chr9:79008512-79009691	A549	lung:	n/a	n/a
32	POLR2A	chr9:79008469-79010318	Hela-S3	cervix:	n/a	n/a
33	ATF2	chr9:79008405-79009087	GM12878	blood:	n/a	n/a
34	ZEB1	chr9:79008569-79009490	GM12878	blood:	n/a	chr9:79008999-79009008
35	MYC	chr9:79008549-79009968	MCF10A-Er-Src	breast:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
36	POLR2A	chr9:79008563-79010148	Raji	blood:	n/a	n/a
37	BATF	chr9:79008528-79008873	GM12878	blood:	n/a	n/a
38	MAX	chr9:79008424-79009858	HCT-116	colon:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
39	PAX5	chr9:79008458-79009561	GM12878	blood:	n/a	chr9:79008720-79008739
40	POLR2A	chr9:79008535-79010164	Hela-S3	cervix:	n/a	n/a
41	EP300	chr9:79008512-79008932	GM12878	blood:	n/a	n/a
42	RUNX3	chr9:79008487-79009990	GM12878	blood:	n/a	n/a
43	MAX	chr9:79008577-79009758	H1-hESC	embryonic stem cell:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
44	USF1	chr9:79008613-79009647	HCT-116	colon:	n/a	chr9:79008940-79008956
45	MAX	chr9:79008513-79009143	SK-N-SH	brain:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
46	E2F6	chr9:79008515-79010217	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr9:79008626-79008824	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr9:79008576-79009779	A549	lung:	n/a	n/a
49	MAX	chr9:79008533-79010184	Hela-S3	cervix:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
50	POLR2A	chr9:79008591-79010170	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79007540..79010172-chr9:79074126..79075718,2	MCF-7	breast:
2	chr9:79007886..79011336-chr9:79013243..79018063,7	MCF-7	breast:

Variant related genes	Relation type
RPSAP9	TF binding region
ENSG00000187210	Chromatin interaction
ENSG00000234618	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10116800	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10118954	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10119732	0.84[ASN][1000 genomes]
rs10125012	0.89[ASN][1000 genomes]
rs10125667	0.89[ASN][1000 genomes]
rs10781358	0.89[ASN][1000 genomes]
rs10781359	0.84[ASN][1000 genomes]
rs10781360	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10869770	0.89[ASN][1000 genomes]
rs10869774	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11144870	0.89[ASN][1000 genomes]
rs11144875	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11144878	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11144881	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11144887	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11144894	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11144897	0.84[ASN][1000 genomes]
rs1129399	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11548954	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791951	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11793613	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11794019	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12156473	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12375735	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12377856	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12377878	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12380522	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1324213	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1951910	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2377640	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2377641	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3187236	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4571791	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55740812	0.82[ASN][1000 genomes]
rs57480680	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58136435	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59424752	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61334567	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62567918	0.82[ASN][1000 genomes]
rs62568690	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62568692	0.89[ASN][1000 genomes]
rs6560513	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6560515	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6560516	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7023191	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7025942	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7026067	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7029439	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7035385	0.89[ASN][1000 genomes]
rs7037345	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7038009	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7040138	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7041690	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7047489	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7049245	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7851616	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7852884	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7853410	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7859327	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7875575	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv3326861	chr9:79008157-79010705	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 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	chr9:79007200-79010000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr9:79007400-79009800	Active TSS	Duodenum Mucosa	Duodenum
3	chr9:79007400-79010200	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr9:79007600-79008800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:79007600-79010000	Active TSS	GM12878-XiMat	blood
6	chr9:79007600-79010000	Active TSS	HMEC	breast
7	chr9:79007600-79010200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:79007600-79010400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:79007600-79010400	Active TSS	NHDF-Ad	bronchial
10	chr9:79007600-79010600	Active TSS	NHEK	skin
11	chr9:79007600-79010800	Active TSS	Brain Anterior Caudate	brain
12	chr9:79007800-79008800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr9:79007800-79008800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:79007800-79010000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:79007800-79010000	Active TSS	Fetal Brain Female	brain
16	chr9:79007800-79010200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:79007800-79010200	Active TSS	Fetal Intestine Large	intestine
18	chr9:79007800-79010200	Active TSS	Fetal Intestine Small	intestine
19	chr9:79007800-79010400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr9:79007800-79010400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr9:79007800-79010400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr9:79007800-79010400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr9:79007800-79010400	Active TSS	Colonic Mucosa	Colon
24	chr9:79007800-79010400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr9:79007800-79010400	Active TSS	A549	lung
26	chr9:79007800-79010400	Active TSS	K562	blood
27	chr9:79007800-79010600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:79008000-79008800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr9:79008000-79008800	Flanking Active TSS	Liver	Liver
30	chr9:79008000-79010200	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr9:79008000-79010400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:79008000-79010400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:79008000-79010600	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr9:79008200-79009600	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr9:79008200-79009800	Active TSS	HUVEC	blood vessel
36	chr9:79008200-79010000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:79008200-79010000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:79008200-79010000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:79008200-79010000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr9:79008200-79010000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:79008200-79010000	Active TSS	Hela-S3	cervix
42	chr9:79008200-79010200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:79008200-79010200	Active TSS	Stomach Smooth Muscle	stomach
44	chr9:79008200-79010400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr9:79008200-79010400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:79008200-79010400	Active TSS	Colon Smooth Muscle	Colon
47	chr9:79008200-79010400	Active TSS	HSMM	muscle
48	chr9:79008200-79010400	Active TSS	HSMMtube	muscle
49	chr9:79008400-79008800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr9:79008400-79008800	Flanking Active TSS	Primary B cells from peripheral blood	blood

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