Variant report

Variant	rs3846484
Chromosome Location	chr5:68469058-68469059
allele	C/T
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:2)
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	chr5:68468836-68469313	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:68468886-68469402	K562	blood:	n/a	n/a
3	POLR2A	chr5:68468829-68469430	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:68468818-68469093	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:68468808-68469174	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:68468925-68469312	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:68468862-68469188	U87	brain:	n/a	n/a
8	POLR2A	chr5:68468942-68469064	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:68468867-68469379	K562	blood:	n/a	n/a
10	POLR2A	chr5:68468961-68469178	MCF-7	breast:	n/a	n/a
11	POLR2A	chr5:68468862-68469138	U87	brain:	n/a	n/a
12	POLR2A	chr5:68468888-68469670	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68393389..68395776-chr5:68467195..68469361,2	K562	blood:
2	chr5:68467066..68470056-chr5:68482970..68485828,3	MCF-7	breast:

No data

Variant related genes	Relation type
CCNB1	TF binding region
ENSG00000153044	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10454825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10515100	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10940208	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1128761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12188874	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189395	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16875380	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17271735	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17271763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17271912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17331590	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2069432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28616082	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3966728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41392244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56072942	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56101109	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56667192	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57047253	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58176819	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58725071	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59497209	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61626775	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61699334	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61743885	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66525615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66595384	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67275234	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67548500	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67693452	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67821207	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67980996	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6867050	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6890817	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767813	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767816	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767820	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767822	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767833	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72767837	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767849	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767855	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767860	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767861	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767863	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767864	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767865	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7709090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7714908	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7734513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3846484	CCDC125	cis	lung	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68463600-68470000	Weak transcription	Ovary	ovary
2	chr5:68463800-68470800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:68463800-68484400	Weak transcription	Adipose Nuclei	Adipose
4	chr5:68463800-68484400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:68463800-68484400	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:68464000-68470000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:68464000-68470000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:68464000-68470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:68464000-68470000	Weak transcription	Placenta	Placenta
10	chr5:68464000-68470000	Weak transcription	Spleen	Spleen
11	chr5:68464000-68470200	Weak transcription	Brain Substantia Nigra	brain
12	chr5:68464000-68470200	Weak transcription	Lung	lung
13	chr5:68464000-68470800	Weak transcription	Liver	Liver
14	chr5:68464000-68470800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:68464000-68471000	Weak transcription	Brain Angular Gyrus	brain
16	chr5:68464000-68472800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:68464000-68473000	Weak transcription	Esophagus	oesophagus
18	chr5:68464000-68473400	Weak transcription	Fetal Brain Male	brain
19	chr5:68464000-68475000	Weak transcription	Colonic Mucosa	Colon
20	chr5:68464000-68476200	Weak transcription	Stomach Mucosa	stomach
21	chr5:68464000-68478000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:68464000-68478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:68464000-68484400	Weak transcription	Pancreas	Pancrea
24	chr5:68464000-68484600	Weak transcription	Right Atrium	heart
25	chr5:68464200-68470000	Weak transcription	Gastric	stomach
26	chr5:68464200-68470800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr5:68464200-68470800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:68464200-68471000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:68464200-68474000	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr5:68464200-68474000	Weak transcription	Small Intestine	intestine
31	chr5:68464200-68474600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:68464200-68484600	Weak transcription	Left Ventricle	heart
33	chr5:68464400-68469200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:68464400-68470600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr5:68464400-68470800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:68464400-68471000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr5:68464400-68473200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:68464400-68473200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:68464400-68473600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:68464400-68479000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr5:68464400-68484400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:68464600-68469400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:68464600-68470000	Weak transcription	Fetal Brain Female	brain
44	chr5:68464600-68470800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:68464600-68473600	Strong transcription	Fetal Muscle Leg	muscle
46	chr5:68464600-68484400	Weak transcription	HSMMtube	muscle
47	chr5:68464800-68474000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr5:68464800-68474400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:68464800-68474400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:68464800-68474600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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