Variant report

Variant	rs72875111
Chromosome Location	chr2:47293362-47293363
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	POLR2A	chr2:47292816-47293653	U87	brain:	n/a	n/a
2	RAD21	chr2:47292983-47293600	SK-N-SH_RA	brain:	n/a	n/a
3	MAX	chr2:47292843-47293367	ECC-1	luminal epithelium:	n/a	n/a
4	RCOR1	chr2:47292460-47293966	IMR90	lung:	n/a	n/a
5	FOSL2	chr2:47292977-47293592	SK-N-SH	brain:	n/a	chr2:47293536-47293544 chr2:47293535-47293545
6	TEAD4	chr2:47292864-47293835	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr2:47292479-47293831	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr2:47293064-47293641	IMR90	lung:	n/a	chr2:47293604-47293613
9	CTCF	chr2:47293360-47293510	WI-38	lung:	n/a	n/a
10	TCF12	chr2:47292829-47293840	SK-N-SH	brain:	n/a	n/a
11	RXRA	chr2:47292900-47293715	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr2:47292786-47293775	SK-N-SH	brain:	n/a	chr2:47293300-47293309
13	PBX3	chr2:47292727-47293779	SK-N-SH	brain:	n/a	n/a
14	GATA2	chr2:47293085-47293551	HUVEC	blood vessel:	n/a	chr2:47293295-47293309 chr2:47293300-47293309
15	POLR2A	chr2:47293130-47293481	HUVEC	blood vessel:	n/a	n/a
16	EP300	chr2:47292840-47293788	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr2:47293085-47293443	HUVEC	blood vessel:	n/a	n/a
18	MAX	chr2:47292751-47293512	A549	lung:	n/a	n/a
19	TEAD4	chr2:47292799-47293736	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr2:47292950-47293592	HUVEC	blood vessel:	n/a	n/a
21	FOSL2	chr2:47292889-47293724	SK-N-SH	brain:	n/a	chr2:47293536-47293544 chr2:47293535-47293545
22	CTCF	chr2:47293240-47293390	AG04449	skin:	n/a	n/a
23	CTCF	chr2:47293240-47293390	HPAF	blood vessel:	n/a	n/a
24	NFIC	chr2:47292666-47293761	SK-N-SH	brain:	n/a	n/a
25	USF1	chr2:47293087-47293389	SK-N-SH_RA	brain:	n/a	n/a
26	MAX	chr2:47292470-47293617	A549	lung:	n/a	n/a
27	EP300	chr2:47292731-47293839	SK-N-SH	brain:	n/a	n/a
28	RXRA	chr2:47292577-47293871	SK-N-SH	brain:	n/a	n/a
29	USF2	chr2:47293113-47293377	Hela-S3	cervix:	n/a	chr2:47293240-47293251
30	POLR2A	chr2:47292798-47293637	SK-N-SH	brain:	n/a	n/a
31	MAX	chr2:47292840-47293655	SK-N-SH	brain:	n/a	n/a
32	REST	chr2:47293107-47293453	SK-N-SH	brain:	n/a	n/a
33	EP300	chr2:47293066-47293440	SK-N-SH_RA	brain:	n/a	n/a
34	MYC	chr2:47293178-47293483	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr2:47293042-47293422	U87	brain:	n/a	n/a
36	CTCF	chr2:47293220-47293370	BJ	skin:	n/a	n/a
37	MAX	chr2:47292776-47293709	SK-N-SH	brain:	n/a	n/a
38	SIN3AK20	chr2:47293085-47293407	SK-N-SH	brain:	n/a	n/a
39	TCF12	chr2:47292625-47293887	SK-N-SH	brain:	n/a	n/a
40	NFIC	chr2:47292808-47293537	SK-N-SH	brain:	n/a	n/a
41	SMC3	chr2:47293211-47293410	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:47292806-47293661	ProgFib	skin:	n/a	n/a
43	POLR2A	chr2:47292905-47293505	IMR90	lung:	n/a	n/a
44	REST	chr2:47293027-47293501	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr2:47293280-47293430	A549	lung:	n/a	n/a
46	JUND	chr2:47292907-47293690	SK-N-SH	brain:	n/a	chr2:47293536-47293544 chr2:47293535-47293545
47	TEAD4	chr2:47293028-47293433	H1-hESC	embryonic stem cell:	n/a	n/a
48	USF1	chr2:47292972-47293484	SK-N-SH	brain:	n/a	n/a
49	GATA3	chr2:47292820-47293764	SK-N-SH	brain:	n/a	chr2:47293300-47293309
50	CTCF	chr2:47293320-47293470	AG09309	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47288795..47291567-chr2:47291902..47294947,3	K562	blood:
2	chr2:47292470..47294231-chr2:47312164..47314753,2	K562	blood:
3	chr2:47292091..47294356-chr2:47400826..47402359,2	K562	blood:
4	chr2:47287750..47290295-chr2:47291902..47294626,3	K562	blood:

Variant related genes	Relation type
ENSG00000225187	TF binding region
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17036223	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17036229	1.00[AMR][1000 genomes]
rs57047194	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57558077	1.00[AMR][1000 genomes]
rs57590657	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58098113	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59510879	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72875114	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72877003	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:47270800-47296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:47282000-47293400	Enhancers	Brain Substantia Nigra	brain
5	chr2:47284400-47296400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:47284400-47296400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:47284600-47296000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:47284600-47298400	Strong transcription	Thymus	Thymus
9	chr2:47285000-47295000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:47285000-47295200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:47285000-47295400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:47285200-47295800	Strong transcription	Primary T cells from cord blood	blood
13	chr2:47286400-47295400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:47286600-47295000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:47286800-47296000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:47286800-47296600	Strong transcription	Fetal Thymus	thymus
17	chr2:47287400-47296200	Strong transcription	Primary B cells from cord blood	blood
18	chr2:47287600-47293400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:47287800-47294600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:47287800-47296600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr2:47288000-47293800	Enhancers	Stomach Mucosa	stomach
22	chr2:47288000-47295000	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr2:47288000-47300400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:47288400-47293800	Enhancers	HSMMtube	muscle
25	chr2:47288400-47296400	Enhancers	Fetal Heart	heart
26	chr2:47289200-47293400	Enhancers	Brain Cingulate Gyrus	brain
27	chr2:47289200-47293400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:47289400-47293600	Enhancers	Brain Anterior Caudate	brain
29	chr2:47289400-47294600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:47289600-47295000	Weak transcription	Gastric	stomach
31	chr2:47290200-47295800	Genic enhancers	HepG2	liver
32	chr2:47290400-47299000	Genic enhancers	Fetal Muscle Leg	muscle
33	chr2:47290600-47293600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:47290600-47294200	Enhancers	HSMM	muscle
35	chr2:47290600-47296400	Genic enhancers	A549	lung
36	chr2:47290800-47297800	Genic enhancers	Primary monocytes fromperipheralblood	blood
37	chr2:47291000-47296200	Genic enhancers	Monocytes-CD14+_RO01746	blood
38	chr2:47291400-47296600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:47291600-47293400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr2:47291600-47293600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr2:47291600-47293600	Enhancers	Brain Hippocampus Middle	brain
42	chr2:47291600-47296200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:47291600-47300800	Weak transcription	Brain Germinal Matrix	brain
44	chr2:47291800-47293800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:47291800-47293800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr2:47291800-47296600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:47291800-47297800	Genic enhancers	Spleen	Spleen
48	chr2:47291800-47301200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr2:47292000-47294000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:47292000-47294200	Enhancers	NHLF	lung

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