Variant report

Variant	rs13373816
Chromosome Location	chr1:227922142-227922143
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227922095-227923743	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:227922135-227923848	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:227921936-227924227	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr1:227921582-227923837	IMR90	lung:	n/a	n/a
5	POLR2A	chr1:227921962-227923649	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:227922134-227923498	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr1:227922088-227923604	GM12891	blood:	n/a	n/a
8	POLR2A	chr1:227922080-227923603	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr1:227922079-227924238	MCF10A-Er-Src	breast:	n/a	n/a
10	MAX	chr1:227922084-227923421	K562	blood:	n/a	chr1:227922598-227922607
11	JUN	chr1:227921816-227924147	K562	blood:	n/a	n/a
12	POLR2A	chr1:227922056-227923512	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227921116..227923050-chr1:228289460..228292114,2	MCF-7	breast:
2	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
3	chr1:227750240..227752795-chr1:227921793..227923560,2	K562	blood:
4	chr1:227921956..227924183-chr1:227932541..227935696,3	MCF-7	breast:
5	chr1:227921488..227923041-chr1:228269667..228272192,2	MCF-7	breast:
6	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:

No data

Variant related genes	Relation type
JMJD4	TF binding region
SNAP47	TF binding region
ENSG00000143761	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000181450	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000230005	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12563117	1.00[EUR][1000 genomes]
rs12563564	1.00[EUR][1000 genomes]
rs12564736	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564917	1.00[EUR][1000 genomes]
rs12564929	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565099	1.00[EUR][1000 genomes]
rs12565109	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12565618	1.00[EUR][1000 genomes]
rs12565653	1.00[EUR][1000 genomes]
rs12566390	1.00[EUR][1000 genomes]
rs12566716	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566948	1.00[ASN][1000 genomes]
rs12567084	1.00[EUR][1000 genomes]
rs12567160	1.00[EUR][1000 genomes]
rs12567934	1.00[EUR][1000 genomes]
rs12568707	1.00[EUR][1000 genomes]
rs1323021	1.00[EUR][1000 genomes]
rs16841323	1.00[EUR][1000 genomes]
rs16847926	1.00[EUR][1000 genomes]
rs16847929	1.00[EUR][1000 genomes]
rs16847948	1.00[EUR][1000 genomes]
rs16847987	1.00[EUR][1000 genomes]
rs16848026	1.00[EUR][1000 genomes]
rs16848044	1.00[EUR][1000 genomes]
rs16848160	1.00[EUR][1000 genomes]
rs16860227	1.00[EUR][1000 genomes]
rs17492440	1.00[EUR][1000 genomes]
rs17492447	1.00[EUR][1000 genomes]
rs2101862	1.00[EUR][1000 genomes]
rs2313220	1.00[EUR][1000 genomes]
rs34560898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34984248	1.00[EUR][1000 genomes]
rs35703429	1.00[EUR][1000 genomes]
rs41305134	1.00[ASN][1000 genomes]
rs4462138	1.00[EUR][1000 genomes]
rs59461077	1.00[EUR][1000 genomes]
rs60156730	1.00[ASN][1000 genomes]
rs6665512	1.00[EUR][1000 genomes]
rs6684706	1.00[ASN][1000 genomes]
rs73090936	1.00[EUR][1000 genomes]
rs73090937	1.00[EUR][1000 genomes]
rs73090938	1.00[EUR][1000 genomes]
rs73090948	1.00[EUR][1000 genomes]
rs73090952	1.00[EUR][1000 genomes]
rs73090985	1.00[EUR][1000 genomes]
rs73090986	1.00[EUR][1000 genomes]
rs73090987	1.00[EUR][1000 genomes]
rs73090994	1.00[EUR][1000 genomes]
rs73091000	1.00[EUR][1000 genomes]
rs73092607	1.00[EUR][1000 genomes]
rs73092610	1.00[EUR][1000 genomes]
rs7554851	1.00[EUR][1000 genomes]
rs996226	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv3387540	chr1:227919379-227922177	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a
9	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	esv3375515	chr1:227921854-227924702	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227921200-227922200	Enhancers	Primary B cells from peripheral blood	blood
2	chr1:227921200-227922200	Weak transcription	Aorta	Aorta
3	chr1:227921400-227922200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:227921400-227922200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:227921400-227922600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:227921600-227922200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:227921600-227922200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:227921600-227922200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr1:227921600-227922200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:227921600-227922200	Enhancers	Esophagus	oesophagus
11	chr1:227921600-227922200	Enhancers	Fetal Heart	heart
12	chr1:227921600-227922200	Enhancers	Lung	lung
13	chr1:227921600-227922200	Enhancers	Right Atrium	heart
14	chr1:227921600-227922200	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr1:227921600-227922200	Enhancers	Stomach Mucosa	stomach
16	chr1:227921600-227922200	Flanking Active TSS	NHEK	skin
17	chr1:227921600-227922200	Flanking Active TSS	NHLF	lung
18	chr1:227921600-227922400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:227921600-227922400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:227921600-227922400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:227921600-227922400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr1:227921600-227922400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:227921600-227922400	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr1:227921600-227922400	Flanking Active TSS	Fetal Thymus	thymus
25	chr1:227921600-227922400	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr1:227921600-227922400	Enhancers	Small Intestine	intestine
27	chr1:227921600-227922600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr1:227921600-227922600	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr1:227921600-227922600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:227921600-227922600	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr1:227921600-227922600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr1:227921600-227922600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr1:227921600-227923000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:227921600-227923000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:227921600-227923600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:227921600-227923600	Active TSS	Placenta Amnion	Placenta Amnion
37	chr1:227921600-227924200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr1:227921600-227924200	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:227921800-227922200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:227921800-227922200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:227921800-227922200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:227921800-227922200	Active TSS	Brain Substantia Nigra	brain
43	chr1:227921800-227922200	Active TSS	Colonic Mucosa	Colon
44	chr1:227921800-227922200	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr1:227921800-227922200	Flanking Active TSS	HSMMtube	muscle
46	chr1:227921800-227922200	Flanking Active TSS	Osteobl	bone
47	chr1:227921800-227922400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:227921800-227922400	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr1:227921800-227922400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr1:227921800-227922400	Flanking Active TSS	HUVEC	blood vessel

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