Variant report

Variant	rs1790062
Chromosome Location	chr11:72928925-72928926
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	MAX	chr11:72928859-72929954	HepG2	liver:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
2	NR2F2	chr11:72928814-72929956	MCF-7	breast:	n/a	n/a
3	REST	chr11:72927508-72930052	HL-60	blood:	n/a	chr11:72929349-72929362 chr11:72929861-72929874 chr11:72929422-72929432 chr11:72929308-72929321 chr11:72929209-72929222 chr11:72928986-72928999
4	BCL3	chr11:72928891-72929855	A549	lung:	n/a	chr11:72929210-72929223 chr11:72929576-72929584
5	SIN3AK20	chr11:72928473-72930107	MCF-7	breast:	n/a	n/a
6	E2F6	chr11:72928888-72929803	H1-hESC	embryonic stem cell:	n/a	chr11:72929309-72929318
7	GABPA	chr11:72928746-72929835	MCF-7	breast:	n/a	chr11:72929559-72929568 chr11:72929309-72929318
8	MAX	chr11:72928827-72929879	HepG2	liver:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
9	ZBTB7A	chr11:72928799-72930172	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr11:72928912-72929865	ECC-1	luminal epithelium:	n/a	n/a
11	ZBTB7A	chr11:72928782-72930163	ECC-1	luminal epithelium:	n/a	n/a
12	GATA3	chr11:72928876-72929842	A549	lung:	n/a	n/a
13	HA-E2F1	chr11:72928922-72929839	MCF-7	breast:	n/a	chr11:72929309-72929318
14	SMARCC1	chr11:72928745-72929844	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr11:72926165-72938018	HL-60	blood:	n/a	n/a
16	CTCF	chr11:72928925-72930692	A549	lung:	n/a	n/a
17	E2F6	chr11:72928859-72929882	A549	lung:	n/a	chr11:72929309-72929318
18	MAX	chr11:72928858-72930044	HCT-116	colon:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929978-72929988 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
19	MAX	chr11:72928890-72930056	ECC-1	luminal epithelium:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929978-72929988 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
20	MYC	chr11:72928514-72929855	NB4	blood:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
21	MAX	chr11:72928875-72929984	ECC-1	luminal epithelium:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
22	MAX	chr11:72928799-72930091	A549	lung:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929978-72929988 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
23	MAX	chr11:72928462-72930057	A549	lung:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929978-72929988 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
24	ZNF263	chr11:72928754-72929807	HEK293-T-REx	kidney:	n/a	n/a
25	POLR2A	chr11:72926306-72930248	NB4	blood:	n/a	n/a
26	TBP	chr11:72928920-72929699	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF12	chr11:72928472-72929889	A549	lung:	n/a	chr11:72929548-72929555
28	MAX	chr11:72928862-72930010	MCF-7	breast:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929978-72929988 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
29	POLR2A	chr11:72926198-72937963	HL-60	blood:	n/a	n/a
30	MAX	chr11:72928913-72930021	MCF-7	breast:	n/a	chr11:72929376-72929386 chr11:72929379-72929386 chr11:72929978-72929988 chr11:72929378-72929388 chr11:72929378-72929387 chr11:72929314-72929324 chr11:72929377-72929388
31	ELF1	chr11:72928844-72929734	MCF-7	breast:	n/a	chr11:72929396-72929408

No.	Distal block	Cell Line	Cell type
1	chr11:72493156..72495189-chr11:72928478..72930668,3	MCF-7	breast:
2	chr11:72534881..72536815-chr11:72928046..72930030,2	MCF-7	breast:
3	chr11:72525940..72528822-chr11:72928585..72931110,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215841	TF binding region
P2RY2	TF binding region
ENSG00000265064	Chromatin interaction
ENSG00000168010	Chromatin interaction
ENSG00000214530	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1613420	1.00[AFR][1000 genomes]
rs1790084	0.86[AFR][1000 genomes]
rs2510880	1.00[AFR][1000 genomes]
rs2510884	1.00[AFR][1000 genomes]
rs4944824	1.00[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053737	chr11:72838564-72956847	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv832208	chr11:72876184-73091003	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
3	nsv1038032	chr11:72925347-72966442	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72925400-72929200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr11:72927600-72929400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr11:72927800-72929000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:72927800-72929000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:72927800-72929000	Enhancers	Brain Substantia Nigra	brain
6	chr11:72927800-72929200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr11:72928000-72929000	Enhancers	Gastric	stomach
8	chr11:72928000-72929000	Enhancers	Ovary	ovary
9	chr11:72928000-72929000	Enhancers	Right Atrium	heart
10	chr11:72928000-72929200	Enhancers	Brain Angular Gyrus	brain
11	chr11:72928200-72929000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:72928200-72929000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr11:72928200-72929000	Enhancers	Brain Hippocampus Middle	brain
14	chr11:72928200-72929200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr11:72928200-72929200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr11:72928200-72929200	Flanking Bivalent TSS/Enh	HepG2	liver
17	chr11:72928200-72930600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:72928400-72929000	Enhancers	Brain Cingulate Gyrus	brain
19	chr11:72928400-72929000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:72928400-72929000	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr11:72928400-72929000	Enhancers	Lung	lung
22	chr11:72928400-72929000	Flanking Active TSS	A549	lung
23	chr11:72928400-72929000	Enhancers	K562	blood
24	chr11:72928400-72930400	Flanking Active TSS	HMEC	breast
25	chr11:72928600-72929000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr11:72928600-72929000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:72928600-72929000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:72928600-72929000	Flanking Active TSS	Fetal Intestine Large	intestine
29	chr11:72928600-72929000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr11:72928600-72929000	Flanking Active TSS	NHEK	skin
31	chr11:72928600-72929200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
32	chr11:72928600-72929200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:72928600-72929200	Flanking Active TSS	Liver	Liver
34	chr11:72928600-72929200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
35	chr11:72928600-72929200	Flanking Active TSS	Placenta	Placenta
36	chr11:72928600-72929200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr11:72928600-72929200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr11:72928600-72929200	Bivalent Enhancer	Stomach Mucosa	stomach
39	chr11:72928600-72930000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
40	chr11:72928600-72930000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr11:72928600-72930000	Enhancers	Fetal Heart	heart
42	chr11:72928600-72930000	Active TSS	Rectal Smooth Muscle	rectum
43	chr11:72928600-72930200	Active TSS	Left Ventricle	heart
44	chr11:72928600-72930400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr11:72928600-72930400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr11:72928600-72930600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr11:72928600-72930600	Active TSS	Psoas Muscle	Psoas
48	chr11:72928800-72929000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:72928800-72929000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
50	chr11:72928800-72929000	Enhancers	Primary hematopoietic stem cells	blood

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