Variant report

Variant	rs7948393
Chromosome Location	chr11:72929447-72929448
allele	C/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	CTCF	chr11:72929392-72929808	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr11:72929440-72929590	HCT-116	colon:	n/a	n/a
3	CTCF	chr11:72929436-72929746	A549	lung:	n/a	n/a
4	HNF4A	chr11:72928999-72929789	HepG2	liver:	n/a	chr11:72929670-72929682 chr11:72929295-72929310 chr11:72929295-72929310 chr11:72929669-72929683 chr11:72929028-72929041 chr11:72929670-72929682 chr11:72929024-72929046 chr11:72929028-72929041 chr11:72929668-72929683 chr11:72929670-72929682
5	RAD21	chr11:72929014-72929857	ECC-1	luminal epithelium:	n/a	chr11:72929311-72929321
6	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
7	TAF1	chr11:72929070-72929742	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr11:72928984-72929885	MCF-7	breast:	n/a	n/a
9	CTCF	chr11:72929430-72929718	GM19238	blood:	n/a	n/a
10	MYC	chr11:72929447-72929755	MCF-7	breast:	n/a	n/a
11	PBX3	chr11:72929085-72929938	A549	lung:	n/a	n/a
12	USF1	chr11:72929202-72929548	SK-N-SH_RA	brain:	n/a	chr11:72929394-72929410
13	POLR2A	chr11:72929057-72929659	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr11:72929418-72929780	NHEK	skin:	n/a	n/a
15	NR2F2	chr11:72928969-72929555	MCF-7	breast:	n/a	n/a
16	ETS1	chr11:72929415-72929836	A549	lung:	n/a	n/a
17	CTCF	chr11:72929446-72929725	MCF-7	breast:	n/a	n/a
18	POLR2A	chr11:72928953-72929714	A549	lung:	n/a	n/a
19	TCF7L2	chr11:72929096-72929818	HCT-116	colon:	n/a	n/a
20	NR2F2	chr11:72928814-72929956	MCF-7	breast:	n/a	n/a
21	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
22	USF2	chr11:72929295-72929480	H1-hESC	embryonic stem cell:	n/a	chr11:72929394-72929410
23	TEAD4	chr11:72929390-72929891	A549	lung:	n/a	n/a
24	BCL3	chr11:72928891-72929855	A549	lung:	n/a	chr11:72929210-72929223 chr11:72929576-72929584
25	GABPA	chr11:72929303-72929788	H1-hESC	embryonic stem cell:	n/a	chr11:72929559-72929568 chr11:72929309-72929318
26	SP1	chr11:72928946-72929759	A549	lung:	n/a	chr11:72929480-72929489 chr11:72929308-72929317 chr11:72928995-72929004 chr11:72929308-72929318 chr11:72929307-72929319 chr11:72929308-72929317 chr11:72929308-72929318 chr11:72929308-72929322 chr11:72929309-72929318 chr11:72929307-72929319
27	SIN3AK20	chr11:72928473-72930107	MCF-7	breast:	n/a	n/a
28	ZNF143	chr11:72929387-72929698	H1-hESC	embryonic stem cell:	n/a	chr11:72929559-72929577
29	POLR2A	chr11:72929129-72929524	MCF-7	breast:	n/a	n/a
30	E2F6	chr11:72928888-72929803	H1-hESC	embryonic stem cell:	n/a	chr11:72929309-72929318
31	SP1	chr11:72928935-72929829	A549	lung:	n/a	chr11:72929480-72929489 chr11:72929308-72929317 chr11:72928995-72929004 chr11:72929308-72929318 chr11:72929307-72929319 chr11:72929308-72929317 chr11:72929308-72929318 chr11:72929308-72929322 chr11:72929309-72929318 chr11:72929307-72929319
32	TCF12	chr11:72929131-72929980	ECC-1	luminal epithelium:	n/a	chr11:72929548-72929555
33	CTCF	chr11:72929440-72929590	HVMF	connective:	n/a	n/a
34	CTCF	chr11:72929400-72929550	WI-38	lung:	n/a	n/a
35	GABPA	chr11:72928746-72929835	MCF-7	breast:	n/a	chr11:72929559-72929568 chr11:72929309-72929318
36	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
37	ZBTB7A	chr11:72928799-72930172	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr11:72929091-72929689	A549	lung:	n/a	n/a
39	CTCF	chr11:72929437-72929740	GM12891	blood:	n/a	n/a
40	USF1	chr11:72929231-72929473	A549	lung:	n/a	chr11:72929394-72929410
41	POLR2A	chr11:72929008-72929882	A549	lung:	n/a	n/a
42	USF1	chr11:72929150-72929953	ECC-1	luminal epithelium:	n/a	chr11:72929394-72929410
43	CTCF	chr11:72929150-72929805	MCF-7	breast:	n/a	n/a
44	TEAD4	chr11:72929137-72929968	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr11:72929052-72929553	HCT-116	colon:	n/a	n/a
46	CTCF	chr11:72929437-72929838	MCF-7	breast:	n/a	n/a
47	CTCF	chr11:72929420-72929687	HepG2	liver:	n/a	n/a
48	TCF12	chr11:72929411-72929640	H1-hESC	embryonic stem cell:	n/a	chr11:72929548-72929555
49	EP300	chr11:72928964-72930031	ECC-1	luminal epithelium:	n/a	chr11:72929234-72929250 chr11:72929971-72929984
50	POLR2A	chr11:72929062-72929626	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:72853154..72855007-chr11:72929139..72931513,2	MCF-7	breast:
2	chr11:72493156..72495189-chr11:72928478..72930668,3	MCF-7	breast:
3	chr11:72929173..72930027-chr11:73000290..73000931,3	MCF-7	breast:
4	chr11:72534881..72536815-chr11:72928046..72930030,2	MCF-7	breast:
5	chr11:72525940..72528822-chr11:72928585..72931110,3	MCF-7	breast:

Variant related genes	Relation type
P2RY2	TF binding region
ENSG00000215841	TF binding region
ENSG00000214530	Chromatin interaction
ENSG00000137478	Chromatin interaction
ENSG00000265064	Chromatin interaction
ENSG00000168010	Chromatin interaction
ENSG00000171631	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs480305	1.00[EUR][1000 genomes]
rs498145	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs498323	1.00[CEU][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs507126	1.00[EUR][1000 genomes]
rs508859	0.85[CEU][hapmap]
rs510921	0.95[EUR][1000 genomes]
rs557451	0.85[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs7934353	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]

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:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72928200-72930600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr11:72928400-72930400	Flanking Active TSS	HMEC	breast
3	chr11:72928600-72930000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr11:72928600-72930000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr11:72928600-72930000	Enhancers	Fetal Heart	heart
6	chr11:72928600-72930000	Active TSS	Rectal Smooth Muscle	rectum
7	chr11:72928600-72930200	Active TSS	Left Ventricle	heart
8	chr11:72928600-72930400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr11:72928600-72930400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr11:72928600-72930600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr11:72928600-72930600	Active TSS	Psoas Muscle	Psoas
12	chr11:72928800-72929600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:72928800-72929600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:72928800-72929600	Bivalent Enhancer	Fetal Thymus	thymus
15	chr11:72928800-72929600	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr11:72928800-72929800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:72928800-72929800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:72928800-72929800	Active TSS	Colon Smooth Muscle	Colon
19	chr11:72928800-72929800	Flanking Active TSS	Spleen	Spleen
20	chr11:72928800-72930000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr11:72928800-72930000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr11:72928800-72930000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:72928800-72930000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:72928800-72930200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr11:72928800-72930200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr11:72928800-72930200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr11:72928800-72930200	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr11:72928800-72930400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
29	chr11:72928800-72930400	Flanking Active TSS	Colonic Mucosa	Colon
30	chr11:72929000-72929600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr11:72929000-72929600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
32	chr11:72929000-72929600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:72929000-72929600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:72929000-72929600	Active TSS	Duodenum Mucosa	Duodenum
35	chr11:72929000-72929600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr11:72929000-72929600	Active TSS	NHEK	skin
37	chr11:72929000-72929800	Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr11:72929000-72929800	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr11:72929000-72930000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:72929000-72930000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:72929000-72930000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:72929000-72930000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:72929000-72930000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:72929000-72930000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:72929000-72930000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:72929000-72930000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:72929000-72930000	Active TSS	Esophagus	oesophagus
48	chr11:72929000-72930000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr11:72929000-72930000	Active TSS	HSMM	muscle
50	chr11:72929000-72930000	Active TSS	Osteobl	bone

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