Variant report

Variant	rs2027538
Chromosome Location	chr10:27530520-27530521
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	POLR2A	chr10:27530275-27530578	A549	lung:	n/a	n/a
2	POLR2A	chr10:27530343-27530613	A549	lung:	n/a	n/a
3	MTA3	chr10:27530146-27530554	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:27530430-27532475	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr10:27529771-27531517	GM12891	blood:	n/a	n/a
6	POLR2A	chr10:27529059-27532978	MCF-7	breast:	n/a	n/a
7	POLR2A	chr10:27529168-27530609	GM12878	blood:	n/a	n/a
8	ZNF384	chr10:27530473-27530670	K562	blood:	n/a	n/a
9	POLR2A	chr10:27529125-27530625	ECC-1	luminal epithelium:	n/a	n/a
10	MTA3	chr10:27529032-27532977	GM12878	blood:	n/a	n/a
11	YY1	chr10:27530455-27531483	GM12892	blood:	n/a	chr10:27531155-27531169 chr10:27531373-27531389
12	YY1	chr10:27530451-27531521	SK-N-SH_RA	brain:	n/a	chr10:27531155-27531169 chr10:27531373-27531389
13	POLR2A	chr10:27529061-27532723	SK-N-MC	brain:	n/a	n/a
14	RELA	chr10:27529936-27531429	GM15510	blood:	n/a	chr10:27530855-27530864 chr10:27530855-27530864
15	UBTF	chr10:27529113-27531425	K562	blood:	n/a	n/a
16	POLR2A	chr10:27529120-27531534	MCF-7	breast:	n/a	n/a
17	POLR2A	chr10:27530262-27531463	K562	blood:	n/a	n/a
18	POLR2A	chr10:27529108-27531463	HL-60	blood:	n/a	n/a
19	POLR2A	chr10:27529167-27532597	Raji	blood:	n/a	n/a
20	MXI1	chr10:27528804-27533681	SK-N-SH	brain:	n/a	n/a
21	ELF1	chr10:27530499-27531564	MCF-7	breast:	n/a	n/a
22	MAX	chr10:27528932-27531588	A549	lung:	n/a	chr10:27530683-27530693
23	POLR2A	chr10:27529206-27532672	GM12878	blood:	n/a	n/a
24	POLR2A	chr10:27529104-27532588	U87	brain:	n/a	n/a
25	MXI1	chr10:27529078-27532630	GM12878	blood:	n/a	n/a
26	MAX	chr10:27529159-27531425	K562	blood:	n/a	chr10:27530683-27530693
27	EP300	chr10:27530454-27531397	ECC-1	luminal epithelium:	n/a	chr10:27530972-27530981 chr10:27531161-27531177
28	TBP	chr10:27529193-27532405	K562	blood:	n/a	chr10:27532336-27532347
29	SIN3A	chr10:27529056-27532474	H1-hESC	embryonic stem cell:	n/a	chr10:27531901-27531910 chr10:27530098-27530107
30	YY1	chr10:27530476-27531525	HepG2	liver:	n/a	chr10:27531155-27531169 chr10:27531373-27531389
31	MYC	chr10:27529128-27531363	NB4	blood:	n/a	chr10:27530683-27530693
32	POLR2A	chr10:27529153-27531513	GM15510	blood:	n/a	n/a
33	POLR2A	chr10:27530376-27532355	IMR90	lung:	n/a	n/a
34	RUNX3	chr10:27529102-27531470	GM12878	blood:	n/a	n/a
35	STAT5A	chr10:27529818-27531494	GM12878	blood:	n/a	chr10:27531057-27531065
36	POLR2A	chr10:27529181-27532999	GM12878	blood:	n/a	n/a
37	BHLHE40	chr10:27530496-27532365	GM12878	blood:	n/a	chr10:27531162-27531178 chr10:27531260-27531276 chr10:27531154-27531170
38	POLR2A	chr10:27529100-27533158	GM12891	blood:	n/a	n/a
39	POLR2A	chr10:27529188-27531449	K562	blood:	n/a	n/a
40	POLR2A	chr10:27529235-27532454	HCT-116	colon:	n/a	n/a
41	TAF1	chr10:27530370-27531448	H1-hESC	embryonic stem cell:	n/a	n/a
42	CHD1	chr10:27530422-27530556	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMC3	chr10:27530466-27530553	K562	blood:	n/a	n/a
44	POLR2A	chr10:27529131-27531452	PANC-1	pancreas:	n/a	n/a
45	REST	chr10:27530485-27531545	A549	lung:	n/a	chr10:27531034-27531047
46	POLR2A	chr10:27529101-27532664	PBDE	blood:	n/a	n/a
47	YY1	chr10:27530412-27531503	GM12878	blood:	n/a	chr10:27531155-27531169 chr10:27531373-27531389
48	SIN3A	chr10:27530012-27531351	GM12878	blood:	n/a	chr10:27530098-27530107
49	POLR2A	chr10:27529171-27532380	K562	blood:	n/a	n/a
50	POLR2A	chr10:27529131-27532458	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:27519329..27521488-chr10:27529432..27532187,2	MCF-7	breast:
2	chr10:27441850..27444956-chr10:27527496..27532549,10	MCF-7	breast:
3	chr10:27529521..27534854-chr10:27538591..27544292,11	K562	blood:
4	chr10:27530518..27532485-chr11:65188635..65191492,2	MCF-7	breast:
5	chr10:27442535..27445982-chr10:27528407..27534290,13	K562	blood:
6	chr10:27523074..27525459-chr10:27528062..27530998,5	K562	blood:
7	chr10:27387680..27390568-chr10:27529145..27530975,2	K562	blood:
8	chr1:118472284..118474004-chr10:27530471..27531974,2	MCF-7	breast:
9	chr10:27481130..27482667-chr10:27530501..27532426,2	K562	blood:
10	chr10:27528592..27532608-chr10:27549768..27554222,6	MCF-7	breast:
11	chr10:27422273..27425391-chr10:27529619..27533685,5	MCF-7	breast:
12	chr10:27425181..27427784-chr10:27528316..27531053,2	MCF-7	breast:
13	chr10:27529491..27532336-chr10:27550751..27553961,4	K562	blood:
14	chr10:27441114..27446089-chr10:27527560..27532728,23	MCF-7	breast:
15	chr10:27442176..27446829-chr10:27524472..27534671,19	K562	blood:

Variant related genes	Relation type
ACBD5	TF binding region
ENSG00000262412	TF binding region
ENSG00000263577	Chromatin interaction
ENSG00000120539	Chromatin interaction
ENSG00000252639	Chromatin interaction
ENSG00000065183	Chromatin interaction
ENSG00000230445	Chromatin interaction
ENSG00000251839	Chromatin interaction
ENSG00000107890	Chromatin interaction
ENSG00000238021	Chromatin interaction
ENSG00000136758	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10829217	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015619	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11015620	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11015624	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11015628	0.94[ASN][1000 genomes]
rs11812283	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812740	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11818418	0.88[ASN][1000 genomes]
rs12260818	0.88[ASN][1000 genomes]
rs12262209	0.88[ASN][1000 genomes]
rs12264871	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12411672	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12415447	0.93[ASN][1000 genomes]
rs12774718	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12775195	0.83[ASN][1000 genomes]
rs12775838	0.88[ASN][1000 genomes]
rs16916444	0.93[ASN][1000 genomes]
rs17748862	0.88[ASN][1000 genomes]
rs1930960	0.88[ASN][1000 genomes]
rs2368220	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34983424	0.88[ASN][1000 genomes]
rs35053986	0.83[ASN][1000 genomes]
rs35931272	0.88[ASN][1000 genomes]
rs3818969	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4747592	1.00[ASN][1000 genomes]
rs4747594	1.00[ASN][1000 genomes]
rs55770293	0.88[ASN][1000 genomes]
rs56207199	0.88[ASN][1000 genomes]
rs56313380	0.88[ASN][1000 genomes]
rs56406502	0.88[ASN][1000 genomes]
rs61149145	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67395401	0.88[ASN][1000 genomes]
rs73598052	0.94[ASN][1000 genomes]
rs7918793	1.00[ASN][1000 genomes]
rs7919198	1.00[ASN][1000 genomes]
rs7919807	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920681	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	esv2422253	chr10:27431366-27575370	Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3337781	chr10:27472216-27666703	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27527800-27532200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr10:27528200-27531800	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr10:27528200-27532400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:27528200-27532400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr10:27528200-27532400	Active TSS	Fetal Kidney	kidney
6	chr10:27528200-27532600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:27528200-27532800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr10:27528400-27532000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr10:27528400-27532000	Active TSS	K562	blood
10	chr10:27528400-27532200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:27528400-27532200	Active TSS	Brain Angular Gyrus	brain
12	chr10:27528400-27532200	Active TSS	Brain Germinal Matrix	brain
13	chr10:27528400-27532200	Active TSS	HepG2	liver
14	chr10:27528400-27532400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:27528400-27532600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr10:27528400-27533000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr10:27528400-27533000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr10:27528600-27530600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr10:27528600-27532000	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr10:27528600-27532000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:27528600-27532000	Active TSS	Left Ventricle	heart
22	chr10:27528600-27532200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:27528600-27532200	Active TSS	Brain Cingulate Gyrus	brain
24	chr10:27528600-27532400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr10:27528600-27532400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr10:27528600-27532400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr10:27528600-27532400	Active TSS	Gastric	stomach
28	chr10:27528600-27532600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr10:27528600-27532600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr10:27528600-27532800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:27528800-27531400	Active TSS	Spleen	Spleen
32	chr10:27528800-27531600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:27528800-27531800	Active TSS	Brain Anterior Caudate	brain
34	chr10:27528800-27531800	Active TSS	Brain Substantia Nigra	brain
35	chr10:27528800-27532000	Active TSS	Fetal Lung	lung
36	chr10:27528800-27532200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:27528800-27532200	Active TSS	Aorta	Aorta
38	chr10:27528800-27532200	Active TSS	Colon Smooth Muscle	Colon
39	chr10:27528800-27532200	Active TSS	Psoas Muscle	Psoas
40	chr10:27528800-27532200	Active TSS	Thymus	Thymus
41	chr10:27528800-27532400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr10:27528800-27532400	Active TSS	Ovary	ovary
43	chr10:27529000-27532000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr10:27529000-27532200	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr10:27529000-27532400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr10:27529000-27532400	Active TSS	Small Intestine	intestine
47	chr10:27529200-27531800	Active TSS	Brain Hippocampus Middle	brain
48	chr10:27529400-27531000	Flanking Active TSS	HMEC	breast
49	chr10:27529600-27532000	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr10:27529800-27530600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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