Variant report

Variant	rs10495579
Chromosome Location	chr2:11272576-11272577
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	chr2:11272471-11273510	MCF-7	breast:	n/a	n/a
2	RAD21	chr2:11272529-11273226	A549	lung:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
3	CTCF	chr2:11272548-11272668	GM10248	blood:	n/a	n/a
4	HCFC1	chr2:11272526-11273409	K562	blood:	n/a	n/a
5	MYBL2	chr2:11272477-11274028	HepG2	liver:	n/a	n/a
6	RAD21	chr2:11272512-11273386	A549	lung:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
7	ELF1	chr2:11272519-11273423	MCF-7	breast:	n/a	n/a
8	POLR2A	chr2:11272390-11272581	GM12878	blood:	n/a	n/a
9	TEAD4	chr2:11272535-11273303	K562	blood:	n/a	n/a
10	CTCF	chr2:11272571-11272663	GM13977	blood:	n/a	n/a
11	CTCF	chr2:11272569-11272677	GM13976	blood:	n/a	n/a
12	CTCF	chr2:11272569-11272668	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr2:11272521-11273550	MCF-7	breast:	n/a	n/a
14	CTCF	chr2:11272555-11272676	GM19238	blood:	n/a	n/a
15	RAD21	chr2:11272431-11273479	HCT-116	colon:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
16	CTCF	chr2:11272197-11273721	SK-N-SH	brain:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
17	ELF1	chr2:11272520-11273180	HepG2	liver:	n/a	n/a
18	RCOR1	chr2:11272558-11273292	HepG2	liver:	n/a	n/a
19	ELF1	chr2:11272478-11273325	MCF-7	breast:	n/a	n/a
20	SMC3	chr2:11272291-11273606	SK-N-SH	brain:	n/a	chr2:11272906-11272920
21	MAZ	chr2:11272454-11273568	IMR90	lung:	n/a	n/a
22	CTCF	chr2:11272520-11272670	GM12874	blood:	n/a	n/a
23	GABPA	chr2:11272540-11273411	MCF-7	breast:	n/a	n/a
24	YY1	chr2:11272451-11273236	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr2:11272343-11273488	A549	lung:	n/a	n/a
26	BCL3	chr2:11272434-11273468	A549	lung:	n/a	chr2:11273187-11273195
27	CTCF	chr2:11272569-11272690	GM19240	blood:	n/a	n/a
28	RCOR1	chr2:11272572-11273309	K562	blood:	n/a	n/a
29	YY1	chr2:11272560-11273200	A549	lung:	n/a	n/a
30	RAD21	chr2:11272452-11273454	HCT-116	colon:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
31	CTCF	chr2:11272500-11272650	AG04449	skin:	n/a	n/a
32	CTCF	chr2:11272329-11273579	A549	lung:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
33	RAD21	chr2:11272206-11273717	SK-N-SH	brain:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
34	CTCF	chr2:11272550-11272650	GM12892	blood:	n/a	n/a
35	SIN3AK20	chr2:11272552-11273500	A549	lung:	n/a	n/a
36	CBX3	chr2:11272526-11273219	K562	blood:	n/a	n/a
37	MXI1	chr2:11272543-11273460	HepG2	liver:	n/a	chr2:11273196-11273211

No.	Distal block	Cell Line	Cell type
1	chr2:11272046..11273363-chr2:11723821..11725006,6	K562	blood:
2	chr2:11272147..11274930-chr2:11671339..11675156,3	MCF-7	breast:
3	chr2:11271098..11275692-chr2:11293512..11297101,4	MCF-7	breast:
4	chr2:10828291..10832221-chr2:11269738..11273006,3	MCF-7	breast:
5	chr2:11269728..11273923-chr2:11678087..11684060,5	MCF-7	breast:
6	chr2:10971180..10977465-chr2:11267266..11272931,15	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ROCK2-3	chr2:11272399-11272896	ENSG00000145063
2	lnc-ROCK2-3	chr2:11272399-11272947	ENSG00000145063.10

Variant related genes	Relation type
ENSG00000145063	TF binding region
C2orf50	TF binding region
ENSG00000243819	Chromatin interaction
ENSG00000239899	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000264010	Chromatin interaction
ENSG00000143870	Chromatin interaction
ENSG00000162976	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10166950	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10166997	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10191933	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11676318	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11678376	1.00[YRI][hapmap]
rs11681385	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13392854	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13399692	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs2357991	0.98[EUR][1000 genomes]
rs28433865	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs55935965	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72785428	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72785429	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10495579	GREB1	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11269800-11274000	Enhancers	Fetal Brain Male	brain
2	chr2:11270400-11272600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:11270400-11272600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:11270400-11272600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:11270400-11272600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:11270400-11272600	Weak transcription	Osteobl	bone
7	chr2:11270400-11272800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:11270400-11272800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:11270400-11273000	Weak transcription	Aorta	Aorta
10	chr2:11270400-11273000	Weak transcription	Esophagus	oesophagus
11	chr2:11270600-11272600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:11270600-11272600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:11270600-11272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:11270600-11272600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:11270600-11272600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:11270600-11272600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:11270600-11272600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:11270600-11272600	Enhancers	Primary T cells from cord blood	blood
19	chr2:11270600-11272600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:11270600-11272600	Weak transcription	Fetal Kidney	kidney
21	chr2:11270600-11272600	Weak transcription	Fetal Lung	lung
22	chr2:11270600-11272600	Weak transcription	Gastric	stomach
23	chr2:11270600-11272600	Weak transcription	Left Ventricle	heart
24	chr2:11270600-11272600	Weak transcription	NH-A	brain
25	chr2:11270600-11272800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:11270600-11272800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:11270600-11272800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:11270600-11272800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:11270600-11272800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:11270600-11272800	Weak transcription	Ovary	ovary
31	chr2:11270600-11272800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:11270600-11272800	Weak transcription	Psoas Muscle	Psoas
33	chr2:11270600-11272800	Weak transcription	Right Atrium	heart
34	chr2:11270600-11272800	Weak transcription	Right Ventricle	heart
35	chr2:11270600-11272800	Weak transcription	HSMM	muscle
36	chr2:11270600-11273000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:11270600-11273000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:11270600-11273000	Weak transcription	Lung	lung
39	chr2:11270600-11273200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr2:11270800-11272600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:11270800-11272600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:11270800-11272600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr2:11270800-11272600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:11270800-11272600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:11270800-11272600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:11270800-11272600	Weak transcription	Liver	Liver
47	chr2:11270800-11272600	Weak transcription	Brain Germinal Matrix	brain
48	chr2:11270800-11272600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr2:11270800-11272600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:11270800-11272600	Weak transcription	A549	lung

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