Variant report

Variant	rs11548954
Chromosome Location	chr9:79009204-79009205
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	chr9:79008660-79010217	NB4	blood:	n/a	n/a
2	CTCF	chr9:79009144-79009462	Spleen_OC	spleen:	n/a	n/a
3	E2F6	chr9:79008627-79009718	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr9:79009142-79009834	PFSK-1	brain:	n/a	n/a
5	CTCF	chr9:79009180-79009330	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr9:79008625-79010078	Gliobla	brain:	n/a	n/a
7	TBP	chr9:79008578-79010208	HepG2	liver:	n/a	n/a
8	ZBTB7A	chr9:79009017-79009528	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr9:79008547-79010015	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:79008482-79010203	Hela-S3	cervix:	n/a	n/a
11	MYC	chr9:79008649-79009598	MCF-7	breast:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
12	TBL1XR1	chr9:79008560-79009977	GM12878	blood:	n/a	n/a
13	SMC3	chr9:79009125-79010177	HepG2	liver:	n/a	n/a
14	POLR2A	chr9:79008604-79010206	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr9:79008961-79009758	K562	blood:	n/a	n/a
16	RXRA	chr9:79009040-79009777	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr9:79009183-79009465	A549	lung:	n/a	n/a
18	MAX	chr9:79008811-79010114	A549	lung:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
19	POLR2A	chr9:79008420-79010195	Hela-S3	cervix:	n/a	n/a
20	REST	chr9:79009183-79009650	PFSK-1	brain:	n/a	n/a
21	YY1	chr9:79009127-79009738	SK-N-SH_RA	brain:	n/a	n/a
22	RELA	chr9:79008531-79010131	GM12892	blood:	n/a	chr9:79009597-79009606 chr9:79009597-79009606
23	ATF3	chr9:79009084-79009589	A549	lung:	n/a	n/a
24	CTCF	chr9:79009200-79009350	GM12872	blood:	n/a	n/a
25	POLR2A	chr9:79008567-79010148	MCF-7	breast:	n/a	n/a
26	SP4	chr9:79009105-79009695	H1-hESC	embryonic stem cell:	n/a	chr9:79009527-79009538
27	MAFK	chr9:79009177-79009469	IMR90	lung:	n/a	n/a
28	MYC	chr9:79008668-79010179	NB4	blood:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
29	CTCF	chr9:79009180-79009330	GM12866	blood:	n/a	n/a
30	ELF1	chr9:79009138-79009711	SK-N-SH	brain:	n/a	chr9:79009681-79009694
31	POLR2A	chr9:79008691-79009715	HUVEC	blood vessel:	n/a	n/a
32	RFX5	chr9:79009185-79010123	HepG2	liver:	n/a	chr9:79009713-79009728 chr9:79009714-79009728
33	MAX	chr9:79008403-79010324	A549	lung:	n/a	chr9:79008962-79008971 chr9:79008961-79008972 chr9:79008915-79008924
34	USF1	chr9:79008639-79009502	ECC-1	luminal epithelium:	n/a	chr9:79008940-79008956
35	EP300	chr9:79009174-79009673	SK-N-SH_RA	brain:	n/a	n/a
36	MXI1	chr9:79009143-79009734	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr9:79009049-79009452	GM12891	blood:	n/a	n/a
38	CTCF	chr9:79009180-79009330	GM12872	blood:	n/a	n/a
39	MYBL2	chr9:79009035-79010199	HepG2	liver:	n/a	n/a
40	RAD21	chr9:79008841-79009500	A549	lung:	n/a	n/a
41	ELF1	chr9:79009083-79009688	K562	blood:	n/a	n/a
42	BHLHE40	chr9:79008570-79009868	GM12878	blood:	n/a	chr9:79008940-79008956
43	POLR2A	chr9:79008707-79010244	K562	blood:	n/a	n/a
44	POLR2A	chr9:79008686-79010202	K562	blood:	n/a	n/a
45	TAF1	chr9:79009106-79009729	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr9:79008640-79009636	HepG2	liver:	n/a	n/a
47	POLR2A	chr9:79009106-79009747	GM12892	blood:	n/a	n/a
48	CTCF	chr9:79009160-79009419	Hela-S3	cervix:	n/a	n/a
49	GTF2F1	chr9:79008911-79009710	H1-hESC	embryonic stem cell:	n/a	n/a
50	RCOR1	chr9:79008427-79010596	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:2328555..2329211-chr9:79008711..79009422,2	Hela-S3	cervix:
2	chr7:92219030..92219725-chr9:79009125..79009872,2	HCT-116	colon:
3	chr9:79007540..79010172-chr9:79074126..79075718,2	MCF-7	breast:
4	chr9:79007886..79011336-chr9:79013243..79018063,7	MCF-7	breast:

Variant related genes	Relation type
RPSAP9	TF binding region
RFK	TF binding region
ENSG00000234618	Chromatin interaction
ENSG00000005206	Chromatin interaction
ENSG00000234545	Chromatin interaction
ENSG00000187210	Chromatin interaction
ENSG00000130332	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	0.89[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[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	0.89[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	0.89[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	0.89[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]
rs62567919	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.89[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	chr9:79007600-79010000	Active TSS	GM12878-XiMat	blood
5	chr9:79007600-79010000	Active TSS	HMEC	breast
6	chr9:79007600-79010200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:79007600-79010400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:79007600-79010400	Active TSS	NHDF-Ad	bronchial
9	chr9:79007600-79010600	Active TSS	NHEK	skin
10	chr9:79007600-79010800	Active TSS	Brain Anterior Caudate	brain
11	chr9:79007800-79010000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:79007800-79010000	Active TSS	Fetal Brain Female	brain
13	chr9:79007800-79010200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:79007800-79010200	Active TSS	Fetal Intestine Large	intestine
15	chr9:79007800-79010200	Active TSS	Fetal Intestine Small	intestine
16	chr9:79007800-79010400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr9:79007800-79010400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr9:79007800-79010400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr9:79007800-79010400	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr9:79007800-79010400	Active TSS	Colonic Mucosa	Colon
21	chr9:79007800-79010400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr9:79007800-79010400	Active TSS	A549	lung
23	chr9:79007800-79010400	Active TSS	K562	blood
24	chr9:79007800-79010600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:79008000-79010200	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr9:79008000-79010400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:79008000-79010400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:79008000-79010600	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr9:79008200-79009600	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr9:79008200-79009800	Active TSS	HUVEC	blood vessel
31	chr9:79008200-79010000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:79008200-79010000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:79008200-79010000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:79008200-79010000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr9:79008200-79010000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:79008200-79010000	Active TSS	Hela-S3	cervix
37	chr9:79008200-79010200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:79008200-79010200	Active TSS	Stomach Smooth Muscle	stomach
39	chr9:79008200-79010400	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr9:79008200-79010400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:79008200-79010400	Active TSS	Colon Smooth Muscle	Colon
42	chr9:79008200-79010400	Active TSS	HSMM	muscle
43	chr9:79008200-79010400	Active TSS	HSMMtube	muscle
44	chr9:79008400-79009400	Active TSS	Brain Germinal Matrix	brain
45	chr9:79008400-79010000	Active TSS	H9 Cell Line	embryonic stem cell
46	chr9:79008400-79010000	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr9:79008400-79010000	Active TSS	Fetal Lung	lung
48	chr9:79008400-79010000	Active TSS	Placenta	Placenta
49	chr9:79008400-79010000	Active TSS	Stomach Mucosa	stomach
50	chr9:79008400-79010000	Active TSS	NHLF	lung

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