Variant report

Variant	rs72907921
Chromosome Location	chr2:38830847-38830848
allele	A/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	chr2:38830540-38830908	A549	lung:	n/a	n/a
2	RAD21	chr2:38830570-38830978	GM12878	blood:	n/a	n/a
3	TCF12	chr2:38830581-38830901	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr2:38830592-38830900	MCF-7	breast:	n/a	n/a
5	STAT5A	chr2:38829889-38830960	GM12878	blood:	n/a	chr2:38830200-38830212
6	SIN3AK20	chr2:38829163-38830978	SK-N-SH	brain:	n/a	n/a
7	EP300	chr2:38829751-38830934	HepG2	liver:	n/a	chr2:38830177-38830193 chr2:38829849-38829858 chr2:38829773-38829789
8	TEAD4	chr2:38829813-38830976	K562	blood:	n/a	n/a
9	RAD21	chr2:38830383-38831116	A549	lung:	n/a	n/a
10	UBTF	chr2:38828546-38830909	K562	blood:	n/a	n/a
11	MAX	chr2:38829019-38831087	HepG2	liver:	n/a	n/a
12	RAD21	chr2:38830555-38830910	SK-N-SH_RA	brain:	n/a	n/a
13	STAT5A	chr2:38829855-38830979	K562	blood:	n/a	chr2:38830200-38830212
14	CTCF	chr2:38830620-38830859	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr2:38830486-38830998	HepG2	liver:	n/a	n/a
16	E2F4	chr2:38829682-38830917	K562	blood:	n/a	chr2:38830234-38830245 chr2:38830233-38830245 chr2:38830237-38830244 chr2:38830237-38830244 chr2:38830237-38830244
17	RCOR1	chr2:38828426-38831063	IMR90	lung:	n/a	n/a
18	TBL1XR1	chr2:38829856-38830998	K562	blood:	n/a	n/a
19	RAD21	chr2:38830565-38830881	K562	blood:	n/a	n/a
20	CTCF	chr2:38830582-38830885	Pancreas_OC	pancreas:	n/a	n/a
21	RAD21	chr2:38830509-38830972	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr2:38830620-38830865	LNCaP	prostate:	n/a	n/a
23	YY1	chr2:38829344-38830866	GM12878	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
24	SIN3AK20	chr2:38828533-38831144	MCF-7	breast:	n/a	n/a
25	RAD21	chr2:38830540-38830944	GM12878	blood:	n/a	n/a
26	CTCF	chr2:38830595-38830882	Kidney_OC	kidney:	n/a	n/a
27	CTCF	chr2:38830700-38830850	HVMF	connective:	n/a	n/a
28	CTCF	chr2:38830584-38830907	HepG2	liver:	n/a	n/a
29	CTCF	chr2:38830504-38830961	A549	lung:	n/a	n/a
30	CTCF	chr2:38830700-38830850	NHDF-neo	bronchial:	n/a	n/a
31	EGR1	chr2:38830505-38830849	K562	blood:	n/a	n/a
32	CTCF	chr2:38830588-38830892	GM12892	blood:	n/a	n/a
33	E2F6	chr2:38829843-38831033	A549	lung:	n/a	chr2:38830233-38830245 chr2:38830237-38830244 chr2:38830237-38830244 chr2:38830237-38830244
34	EGR1	chr2:38829402-38831083	HCT-116	colon:	n/a	chr2:38830139-38830152 chr2:38830140-38830149 chr2:38830134-38830156 chr2:38829801-38829811 chr2:38830139-38830152 chr2:38830138-38830153 chr2:38830139-38830152 chr2:38830138-38830152 chr2:38830139-38830149 chr2:38829798-38829811 chr2:38830140-38830151 chr2:38830139-38830152 chr2:38830136-38830150
35	SIN3AK20	chr2:38829621-38830884	K562	blood:	n/a	n/a
36	CTCF	chr2:38830609-38830883	GM13977	blood:	n/a	n/a
37	CTCF	chr2:38830700-38830850	GM12873	blood:	n/a	n/a
38	POLR2A	chr2:38828985-38830918	H1-neurons	neurons:	n/a	n/a
39	NFATC1	chr2:38830201-38830956	GM12878	blood:	n/a	n/a
40	HA-E2F1	chr2:38829827-38831039	MCF-7	breast:	n/a	chr2:38830233-38830245 chr2:38830237-38830244 chr2:38830237-38830244 chr2:38830237-38830244
41	YY1	chr2:38830530-38830931	GM12878	blood:	n/a	n/a
42	CTCF	chr2:38830590-38830910	Fibrobl	skin:	n/a	n/a
43	CTCF	chr2:38830601-38830889	MCF-7	breast:	n/a	n/a
44	MAX	chr2:38829399-38831046	ECC-1	luminal epithelium:	n/a	n/a
45	CTCF	chr2:38830575-38830854	SK-N-SH_RA	brain:	n/a	n/a
46	WRNIP1	chr2:38830637-38831292	GM12878	blood:	n/a	n/a
47	GABPA	chr2:38830622-38830849	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr2:38829066-38830968	H1-neurons	neurons:	n/a	n/a
49	CTCF	chr2:38830590-38830896	MCF-7	breast:	n/a	n/a
50	FOXA1	chr2:38830640-38830885	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
2	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38823060..38827854-chr2:38827983..38831423,11	MCF-7	breast:
5	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
6	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
7	chr2:38816751..38822030-chr2:38827238..38830922,5	MCF-7	breast:
8	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
9	chr2:38829496..38831232-chr2:38893143..38894875,2	MCF-7	breast:

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000115875	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000232518	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000143889	Chromatin interaction

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

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

rs_ID	r²[population]
rs56686184	1.00[AFR][1000 genomes]
rs57899462	1.00[AFR][1000 genomes]
rs59417682	1.00[AFR][1000 genomes]
rs72905899	1.00[AFR][1000 genomes]
rs72909837	1.00[AFR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38825200-38831000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:38826400-38831400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:38826800-38831000	Active TSS	Duodenum Mucosa	Duodenum
4	chr2:38827000-38831400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr2:38827200-38831000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:38827200-38831000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:38827200-38831000	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr2:38827200-38831200	Active TSS	Brain Germinal Matrix	brain
9	chr2:38827400-38831000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:38827400-38831000	Active TSS	Right Ventricle	heart
11	chr2:38827400-38831200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:38827600-38831000	Active TSS	Brain Anterior Caudate	brain
13	chr2:38827600-38831000	Active TSS	Thymus	Thymus
14	chr2:38827600-38831400	Active TSS	Colonic Mucosa	Colon
15	chr2:38827800-38831000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:38827800-38831000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:38827800-38831000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:38827800-38831000	Active TSS	NHDF-Ad	bronchial
19	chr2:38828000-38831000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr2:38828000-38831000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:38828000-38831000	Active TSS	Brain Hippocampus Middle	brain
22	chr2:38828000-38831000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr2:38828000-38831000	Active TSS	HSMMtube	muscle
24	chr2:38828000-38831200	Active TSS	Psoas Muscle	Psoas
25	chr2:38828000-38831200	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr2:38828000-38831400	Active TSS	Fetal Muscle Trunk	muscle
27	chr2:38828200-38831000	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:38828400-38831200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:38828600-38831000	Active TSS	Fetal Brain Female	brain
30	chr2:38828800-38831000	Active TSS	Adipose Nuclei	Adipose
31	chr2:38828800-38831400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr2:38829200-38831200	Active TSS	Liver	Liver
33	chr2:38829800-38831000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:38829800-38831200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:38830000-38831000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:38830000-38831000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:38830200-38831000	Active TSS	Right Atrium	heart
38	chr2:38830400-38831000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:38830400-38831000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:38830400-38831000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:38830400-38831200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr2:38830400-38831200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr2:38830400-38831200	Flanking Active TSS	GM12878-XiMat	blood
44	chr2:38830400-38831400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr2:38830400-38831400	Flanking Active TSS	Dnd41	blood
46	chr2:38830600-38831000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr2:38830600-38831000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr2:38830600-38831000	Flanking Active TSS	Fetal Stomach	stomach
49	chr2:38830600-38831000	Flanking Active TSS	NH-A	brain
50	chr2:38830600-38831200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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