Variant report

Variant	rs534416
Chromosome Location	chr6:44266925-44266926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:44266562-44266930	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr6:44266580-44267052	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:44264816-44267173	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr6:44266615-44266992	U87	brain:	n/a	n/a
5	POLR2A	chr6:44266611-44267040	U87	brain:	n/a	n/a
6	POLR2A	chr6:44265359-44266934	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr6:44266668-44266970	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:44263937-44267184	K562	blood:	n/a	n/a
9	POLR2A	chr6:44266176-44267029	K562	blood:	n/a	n/a
10	POLR2A	chr6:44265434-44266967	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:44265464-44267000	K562	blood:	n/a	n/a
12	POLR2A	chr6:44266528-44267437	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:44266574-44267059	HL-60	blood:	n/a	n/a
14	POLR2A	chr6:44265867-44267076	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:44265194-44267200	MCF-7	breast:	n/a	n/a
16	POLR2A	chr6:44263749-44267649	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:44266798-44267482	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr6:44265447-44267463	K562	blood:	n/a	n/a
19	POLR2A	chr6:44265031-44267708	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr6:44264694-44267364	K562	blood:	n/a	n/a
21	POLR2A	chr6:44266828-44267054	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:44266610-44267027	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:44265456-44267637	K562	blood:	n/a	n/a
24	POLR2A	chr6:44264588-44267786	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr6:44263985-44267145	GM12892	blood:	n/a	n/a
26	POLR2A	chr6:44266650-44267010	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:44266637-44266980	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr6:44265411-44267001	GM12892	blood:	n/a	n/a
29	POLR2A	chr6:44266767-44267008	HCT-116	colon:	n/a	n/a
30	POLR2A	chr6:44264619-44267120	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:44266710-44266955	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr6:44266562-44267036	GM12891	blood:	n/a	n/a
33	POLR2A	chr6:44263946-44267585	K562	blood:	n/a	n/a
34	POLR2A	chr6:44262608-44267730	K562	blood:	n/a	n/a
35	POLR2A	chr6:44266783-44266963	GM12891	blood:	n/a	n/a
36	POLR2A	chr6:44265261-44266959	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr6:44266560-44267335	PANC-1	pancreas:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44231713..44233466-chr6:44264708..44267385,2	MCF-7	breast:
2	chr6:44250404..44254517-chr6:44264090..44267267,4	MCF-7	breast:
3	chr6:44261562..44267016-chr6:44278207..44281216,9	MCF-7	breast:
4	chr6:44215194..44217832-chr6:44265456..44268236,2	K562	blood:
5	chr6:44257360..44259617-chr6:44265641..44268497,2	MCF-7	breast:

No data

Variant related genes	Relation type
TCTE1	TF binding region
ENSG00000146221	Chromatin interaction
ENSG00000146232	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000124608	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11571907	1.00[ASN][1000 genomes]
rs11571915	1.00[ASN][1000 genomes]
rs11571917	1.00[ASN][1000 genomes]
rs11571951	1.00[ASN][1000 genomes]
rs11571957	1.00[ASN][1000 genomes]
rs11571998	1.00[ASN][1000 genomes]
rs11572002	1.00[ASN][1000 genomes]
rs11572056	1.00[ASN][1000 genomes]
rs12193699	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1293204	1.00[ASN][1000 genomes]
rs1331293	1.00[ASN][1000 genomes]
rs1411905	1.00[ASN][1000 genomes]
rs161706	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324136	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324141	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs324143	0.96[EUR][1000 genomes]
rs325005	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325006	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325007	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325009	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325010	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs325011	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35260018	0.93[EUR][1000 genomes]
rs4308546	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499913	0.84[AFR][1000 genomes]
rs4714775	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4714778	1.00[ASN][1000 genomes]
rs482336	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484757	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs505617	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs511088	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs567192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568902	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61462867	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650075	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927345	1.00[ASN][1000 genomes]
rs7740535	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs865027	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9357439	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9369483	1.00[ASN][1000 genomes]
rs9472241	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9472243	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472244	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
7	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
8	esv1807818	chr6:44266574-44275011	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44265000-44268000	Weak transcription	Dnd41	blood
2	chr6:44265000-44269800	Weak transcription	Hela-S3	cervix
3	chr6:44265400-44268000	Weak transcription	Aorta	Aorta
4	chr6:44265600-44268000	Weak transcription	HepG2	liver
5	chr6:44265600-44268200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:44265600-44279600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:44265800-44268000	Weak transcription	HSMM	muscle
8	chr6:44265800-44269400	Weak transcription	K562	blood
9	chr6:44265800-44270000	Weak transcription	HMEC	breast
10	chr6:44266000-44267800	Weak transcription	Brain Substantia Nigra	brain
11	chr6:44266000-44268000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:44266000-44268000	Weak transcription	Primary T cells from cord blood	blood
13	chr6:44266000-44268000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:44266000-44268000	Weak transcription	Brain Anterior Caudate	brain
15	chr6:44266000-44268000	Weak transcription	Left Ventricle	heart
16	chr6:44266000-44268000	Weak transcription	Ovary	ovary
17	chr6:44266000-44268000	Weak transcription	Right Ventricle	heart
18	chr6:44266000-44268000	Weak transcription	Spleen	Spleen
19	chr6:44266000-44268000	Weak transcription	A549	lung
20	chr6:44266000-44268200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:44266000-44268200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:44266000-44268200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:44266000-44268200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:44266000-44269800	Weak transcription	GM12878-XiMat	blood
25	chr6:44266000-44271600	Weak transcription	NHDF-Ad	bronchial
26	chr6:44266000-44272400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:44266000-44276600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:44266000-44277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:44266000-44280000	Weak transcription	Small Intestine	intestine
30	chr6:44266200-44267400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:44266200-44267400	Weak transcription	Liver	Liver
32	chr6:44266200-44267400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:44266200-44267800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:44266200-44268000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:44266200-44268000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:44266200-44268000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:44266200-44268000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr6:44266200-44268000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:44266200-44268000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:44266200-44268000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:44266200-44268000	Weak transcription	Adipose Nuclei	Adipose
42	chr6:44266200-44268000	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:44266200-44268000	Weak transcription	Pancreas	Pancrea
44	chr6:44266200-44268000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:44266200-44268400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:44266200-44269000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:44266200-44269600	Weak transcription	Fetal Lung	lung
48	chr6:44266200-44269800	Weak transcription	HSMMtube	muscle
49	chr6:44266200-44270000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:44266200-44270800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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