Variant report

Variant	rs11539770
Chromosome Location	chr7:99036649-99036650
allele	C/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	MYC	chr7:99036183-99037033	NB4	blood:	n/a	n/a
2	POLR2A	chr7:99035108-99037621	K562	blood:	n/a	n/a
3	YY1	chr7:99036207-99036978	GM12892	blood:	n/a	chr7:99036541-99036555 chr7:99036625-99036639
4	YY1	chr7:99036265-99036982	A549	lung:	n/a	chr7:99036541-99036555 chr7:99036625-99036639
5	POLR2A	chr7:99036079-99037275	HCT-116	colon:	n/a	n/a
6	MAX	chr7:99036146-99036800	ECC-1	luminal epithelium:	n/a	n/a
7	BCLAF1	chr7:99036145-99036711	GM12878	blood:	n/a	n/a
8	USF1	chr7:99036267-99036662	A549	lung:	n/a	chr7:99036625-99036641
9	POLR2A	chr7:99036153-99037195	HEK293	kidney:	n/a	n/a
10	BHLHE40	chr7:99036233-99036727	GM12878	blood:	n/a	chr7:99036625-99036641
11	POLR2A	chr7:99036023-99037163	MCF-7	breast:	n/a	n/a
12	POLR2A	chr7:99036141-99037006	HepG2	liver:	n/a	n/a
13	MXI1	chr7:99036320-99036801	K562	blood:	n/a	n/a
14	TCF12	chr7:99035907-99036835	A549	lung:	n/a	n/a
15	JUND	chr7:99036094-99036785	A549	lung:	n/a	n/a
16	E2F6	chr7:99036182-99036744	A549	lung:	n/a	chr7:99036626-99036636 chr7:99036541-99036550 chr7:99036407-99036416 chr7:99036632-99036642
17	POLR2A	chr7:99036161-99037274	U87	brain:	n/a	n/a
18	TAF1	chr7:99036170-99036775	H1-neurons	neurons:	n/a	n/a
19	STAT5A	chr7:99036198-99036670	K562	blood:	n/a	chr7:99036245-99036257
20	SP1	chr7:99036112-99037031	A549	lung:	n/a	chr7:99036929-99036941 chr7:99036979-99036993 chr7:99036124-99036136 chr7:99036931-99036940 chr7:99036929-99036941 chr7:99036125-99036134
21	JUND	chr7:99036225-99037172	K562	blood:	n/a	n/a
22	ETS1	chr7:99036334-99036660	A549	lung:	n/a	n/a
23	POLR2A	chr7:99036079-99037059	HUVEC	blood vessel:	n/a	n/a
24	PML	chr7:99036051-99036960	MCF-7	breast:	n/a	n/a
25	PBX3	chr7:99036054-99036701	A549	lung:	n/a	n/a
26	SRF	chr7:99036157-99036829	ECC-1	luminal epithelium:	n/a	chr7:99036626-99036636
27	EP300	chr7:99036254-99036716	SK-N-SH_RA	brain:	n/a	chr7:99036631-99036640 chr7:99036541-99036550
28	POLR2A	chr7:99036127-99037052	GM12878	blood:	n/a	n/a
29	MYC	chr7:99036176-99036947	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr7:99036087-99037072	NB4	blood:	n/a	n/a
31	MYC	chr7:99036240-99036841	K562	blood:	n/a	n/a
32	MAX	chr7:99036208-99036864	GM12878	blood:	n/a	n/a
33	GATA3	chr7:99036079-99036902	A549	lung:	n/a	n/a
34	GABPA	chr7:99036049-99036786	SK-N-SH	brain:	n/a	chr7:99036406-99036415 chr7:99036406-99036420 chr7:99036403-99036417 chr7:99036406-99036417
35	ZBTB7A	chr7:99035944-99036679	K562	blood:	n/a	n/a
36	YY1	chr7:99036283-99036812	ECC-1	luminal epithelium:	n/a	chr7:99036541-99036555 chr7:99036625-99036639
37	IRF1	chr7:99036198-99036943	K562	blood:	n/a	chr7:99036442-99036453 chr7:99036443-99036455
38	REST	chr7:99036106-99036702	MCF-7	breast:	n/a	n/a
39	ETS1	chr7:99036241-99036664	GM12878	blood:	n/a	n/a
40	CREB1	chr7:99036086-99037211	HepG2	liver:	n/a	n/a
41	SRF	chr7:99036027-99037138	MCF-7	breast:	n/a	chr7:99036626-99036636
42	POLR2A	chr7:99036098-99037162	Hela-S3	cervix:	n/a	n/a
43	ETS1	chr7:99036076-99037094	K562	blood:	n/a	n/a
44	MYBL2	chr7:99036010-99037002	HepG2	liver:	n/a	n/a
45	POLR2A	chr7:99036066-99037079	A549	lung:	n/a	n/a
46	REST	chr7:99036350-99036658	PANC-1	pancreas:	n/a	n/a
47	PAX5	chr7:99036289-99036793	GM12892	blood:	n/a	chr7:99036304-99036314
48	YY1	chr7:99036107-99036748	SK-N-SH_RA	brain:	n/a	chr7:99036541-99036555 chr7:99036625-99036639
49	MXI1	chr7:99036184-99037113	HepG2	liver:	n/a	n/a
50	MYC	chr7:99036300-99036840	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:99036051..99038082-chr7:99079952..99081854,3	K562	blood:
2	chr7:99008645..99011330-chr7:99036359..99039743,4	K562	blood:
3	chr7:99034517..99037333-chr7:99070217..99072293,2	K562	blood:
4	chr7:98739484..98741856-chr7:99035435..99038061,2	K562	blood:
5	chr7:99004207..99009187-chr7:99032699..99039268,13	MCF-7	breast:
6	chr7:99036383..99037983-chr7:99697616..99700262,2	MCF-7	breast:
7	chr7:98970707..98973711-chr7:99034539..99037806,4	MCF-7	breast:
8	chr7:99035431..99038374-chr7:99696976..99699327,2	K562	blood:
9	chr7:75544201..75544974-chr7:99036458..99037062,2	NB4	blood:
10	chr7:99005761..99007888-chr7:99034840..99036856,3	K562	blood:
11	chr6:134495044..134495795-chr7:99036121..99037024,2	Hela-S3	cervix:
12	chr7:99003930..99008101-chr7:99034839..99037079,5	K562	blood:
13	chr7:99010009..99013201-chr7:99032916..99037248,5	MCF-7	breast:
14	chr7:99035477..99037165-chr7:100025272..100027414,2	K562	blood:
15	chr7:99034720..99038160-chr7:99048984..99054018,5	MCF-7	breast:
16	chr11:62608557..62609372-chr7:99036141..99036767,2	Hela-S3	cervix:
17	chr7:99004073..99007178-chr7:99034881..99037749,7	MCF-7	breast:
18	chr7:99035887..99038153-chr7:99062281..99064908,3	MCF-7	breast:
19	chr7:99034954..99037866-chr7:99677567..99679393,3	K562	blood:
20	chr7:99034954..99037975-chr7:99677842..99679932,3	K562	blood:
21	chr7:99034906..99037926-chr7:99095119..99098935,4	K562	blood:
22	chr7:99030944..99035080-chr7:99035226..99039444,6	MCF-7	breast:
23	chr7:99035601..99038053-chr7:99042124..99044102,2	MCF-7	breast:
24	chr7:99035600..99037470-chr7:99101229..99103802,2	K562	blood:
25	chr7:99035327..99038027-chr7:99096331..99099819,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214314	TF binding region
CPSF4	TF binding region
PTCD1	TF binding region
ENSG00000241468	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000265020	Chromatin interaction
ENSG00000248919	Chromatin interaction
ENSG00000198742	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000127948	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000198556	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000118515	Chromatin interaction
ENSG00000239133	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000196652	Chromatin interaction
ENSG00000160908	Chromatin interaction
ENSG00000221838	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1002172	0.84[EUR][1000 genomes]
rs1004387	0.83[EUR][1000 genomes]
rs10225314	0.84[EUR][1000 genomes]
rs10240199	0.82[ASN][1000 genomes]
rs10244158	0.82[ASN][1000 genomes]
rs10265385	0.84[ASN][1000 genomes]
rs10271049	0.86[ASN][1000 genomes]
rs1043466	0.81[ASN][1000 genomes]
rs10464604	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538826	0.99[ASN][1000 genomes]
rs13227795	0.81[ASN][1000 genomes]
rs13240600	0.81[ASN][1000 genomes]
rs13437771	0.81[ASN][1000 genomes]
rs17161652	0.92[EUR][1000 genomes]
rs17161677	1.00[EUR][1000 genomes]
rs17161698	1.00[EUR][1000 genomes]
rs17161766	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17161768	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17161769	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17161771	0.84[EUR][1000 genomes]
rs17161772	0.84[EUR][1000 genomes]
rs17161774	0.92[EUR][1000 genomes]
rs17161780	0.92[EUR][1000 genomes]
rs17161783	0.92[EUR][1000 genomes]
rs1980307	0.81[ASN][1000 genomes]
rs1985453	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2057906	1.00[EUR][1000 genomes]
rs2107705	1.00[EUR][1000 genomes]
rs2240384	0.86[ASN][1000 genomes]
rs2240385	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269985	1.00[EUR][1000 genomes]
rs2280600	0.81[ASN][1000 genomes]
rs2280601	0.81[ASN][1000 genomes]
rs2404322	1.00[EUR][1000 genomes]
rs28457808	0.81[ASN][1000 genomes]
rs3764815	1.00[EUR][1000 genomes]
rs3779354	0.82[ASN][1000 genomes]
rs3800960	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3823812	0.92[EUR][1000 genomes]
rs45492098	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45540134	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45622743	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646446	0.92[EUR][1000 genomes]
rs4646447	0.92[EUR][1000 genomes]
rs4646449	0.92[EUR][1000 genomes]
rs4646453	0.92[EUR][1000 genomes]
rs4646456	0.92[EUR][1000 genomes]
rs58024720	0.84[EUR][1000 genomes]
rs58222677	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58421977	1.00[EUR][1000 genomes]
rs59986060	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60301933	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs60865030	0.92[EUR][1000 genomes]
rs61159815	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61337492	0.92[EUR][1000 genomes]
rs61402640	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61543997	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6962772	0.82[ASN][1000 genomes]
rs72494451	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72494452	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73709637	1.00[EUR][1000 genomes]
rs73709641	1.00[EUR][1000 genomes]
rs7794682	0.86[ASN][1000 genomes]
rs7794705	0.83[ASN][1000 genomes]
rs883403	0.83[ASN][1000 genomes]
rs917154	0.81[ASN][1000 genomes]
rs940336	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv888769	chr7:99018584-99041748	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv888770	chr7:99021344-99041748	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 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	chr7:99034800-99038200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:99035200-99037200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr7:99035200-99037400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr7:99035200-99037400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr7:99035200-99037400	Active TSS	Fetal Kidney	kidney
6	chr7:99035200-99037600	Active TSS	A549	lung
7	chr7:99035200-99038600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr7:99035400-99037200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:99035400-99037200	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr7:99035400-99037200	Active TSS	Fetal Heart	heart
11	chr7:99035400-99037400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr7:99035400-99037400	Active TSS	NH-A	brain
13	chr7:99035400-99037400	Active TSS	NHDF-Ad	bronchial
14	chr7:99035400-99037800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr7:99035400-99037800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr7:99035400-99038800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:99035600-99037000	Active TSS	Primary T cells from cord blood	blood
18	chr7:99035600-99037000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:99035600-99037000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr7:99035600-99037200	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr7:99035600-99037200	Active TSS	Brain Hippocampus Middle	brain
22	chr7:99035600-99037200	Active TSS	Brain Substantia Nigra	brain
23	chr7:99035600-99037200	Active TSS	Colon Smooth Muscle	Colon
24	chr7:99035600-99037200	Active TSS	HMEC	breast
25	chr7:99035600-99037400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:99035600-99037400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:99035600-99037400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:99035600-99037400	Active TSS	Gastric	stomach
29	chr7:99035600-99037400	Active TSS	HSMMtube	muscle
30	chr7:99035600-99037600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:99035600-99037600	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr7:99035600-99037800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:99035600-99038200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:99035800-99037000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:99035800-99037000	Active TSS	Brain Angular Gyrus	brain
36	chr7:99035800-99037000	Active TSS	Brain Anterior Caudate	brain
37	chr7:99035800-99037000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr7:99035800-99037000	Active TSS	Duodenum Mucosa	Duodenum
39	chr7:99035800-99037000	Active TSS	Fetal Intestine Small	intestine
40	chr7:99035800-99037000	Active TSS	Fetal Thymus	thymus
41	chr7:99035800-99037000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr7:99035800-99037000	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr7:99035800-99037000	Active TSS	HepG2	liver
44	chr7:99035800-99037000	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr7:99035800-99037200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:99035800-99037200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:99035800-99037200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr7:99035800-99037200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:99035800-99037200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:99035800-99037200	Active TSS	Brain Cingulate Gyrus	brain

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