Variant report

Variant	rs13175606
Chromosome Location	chr5:68465471-68465472
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	chr5:68465458-68465616	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:68465375-68465482	K562	blood:	n/a	n/a
3	POLR2A	chr5:68465140-68465552	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68465113..68468110-chr5:68478273..68481961,4	MCF-7	breast:
2	chr5:68462643..68465474-chr5:68512138..68513918,2	K562	blood:
3	chr5:68463334..68467714-chr5:68469560..68473881,5	MCF-7	breast:

Variant related genes	Relation type
CCNB1	TF binding region
ENSG00000238334	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000134057	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs100192	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10063757	0.88[EUR][1000 genomes]
rs10940209	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940210	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10940212	0.81[ASN][1000 genomes]
rs10940216	0.81[ASN][1000 genomes]
rs11744596	0.83[ASN][1000 genomes]
rs11748974	0.88[ASN][1000 genomes]
rs12659146	0.83[ASN][1000 genomes]
rs151589	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163442	0.85[ASN][1000 genomes]
rs163443	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs163444	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164386	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs164388	0.85[ASN][1000 genomes]
rs164389	0.83[ASN][1000 genomes]
rs164390	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs164709	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs164715	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164789	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1650779	0.94[ASN][1000 genomes]
rs1683831	0.82[ASN][1000 genomes]
rs171212	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs184747	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976103	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2002825	0.83[ASN][1000 genomes]
rs2130757	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2171148	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2172056	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242350	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2242351	0.83[ASN][1000 genomes]
rs2291519	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291520	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2450230	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450246	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2637128	0.82[ASN][1000 genomes]
rs28506805	0.82[ASN][1000 genomes]
rs28602964	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28768211	0.87[EUR][1000 genomes]
rs2930944	0.83[ASN][1000 genomes]
rs2930945	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2930946	0.83[ASN][1000 genomes]
rs2930949	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2930951	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932767	0.93[ASN][1000 genomes]
rs2932770	0.83[ASN][1000 genomes]
rs2932771	0.83[ASN][1000 genomes]
rs2932772	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932773	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932775	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932776	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932777	0.83[ASN][1000 genomes]
rs2932778	0.82[ASN][1000 genomes]
rs2932782	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972358	0.83[ASN][1000 genomes]
rs2972361	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972366	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972373	0.83[ASN][1000 genomes]
rs2972374	0.83[ASN][1000 genomes]
rs2972377	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972378	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2972381	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972386	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972387	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972388	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972390	0.83[ASN][1000 genomes]
rs34845020	0.81[ASN][1000 genomes]
rs34893396	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34935424	0.84[ASN][1000 genomes]
rs350095	0.81[ASN][1000 genomes]
rs350099	0.85[ASN][1000 genomes]
rs350104	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs350105	0.82[ASN][1000 genomes]
rs350106	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs350107	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350109	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350115	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350116	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350119	0.84[ASN][1000 genomes]
rs350120	0.85[ASN][1000 genomes]
rs350122	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350123	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350124	0.83[ASN][1000 genomes]
rs350125	0.81[ASN][1000 genomes]
rs351424	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs352626	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs35308484	0.89[EUR][1000 genomes]
rs353656	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs375285	0.85[ASN][1000 genomes]
rs376768	0.85[ASN][1000 genomes]
rs379106	0.96[ASN][1000 genomes]
rs379434	0.85[ASN][1000 genomes]
rs386640	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389686	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs389938	0.85[ASN][1000 genomes]
rs390169	0.80[ASN][1000 genomes]
rs3934528	0.91[ASN][1000 genomes]
rs395122	0.85[ASN][1000 genomes]
rs4077460	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs419902	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426392	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4266362	0.90[ASN][1000 genomes]
rs4362903	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs437665	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4421064	0.91[ASN][1000 genomes]
rs444305	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4541612	0.89[ASN][1000 genomes]
rs4629549	0.92[ASN][1000 genomes]
rs476125	0.82[ASN][1000 genomes]
rs488498	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4976189	0.84[ASN][1000 genomes]
rs603029	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62373164	0.91[ASN][1000 genomes]
rs6450026	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6450027	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6450029	0.84[ASN][1000 genomes]
rs648489	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs651076	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs676012	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs676879	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6866993	0.92[ASN][1000 genomes]
rs6873869	0.84[ASN][1000 genomes]
rs6876783	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs693725	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719040	0.85[ASN][1000 genomes]
rs7733556	0.92[ASN][1000 genomes]
rs875459	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13175606	CCDC125	cis	Muscle Skeletal	GTEx
rs13175606	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs13175606	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs13175606	TAF9	cis	Esophagus Muscularis	GTEx
rs13175606	CCDC125	cis	lung	GTEx
rs13175606	MRPS36	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68463600-68465600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr5:68463600-68468800	Weak transcription	Aorta	Aorta
3	chr5:68463600-68470000	Weak transcription	Ovary	ovary
4	chr5:68463800-68465600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:68463800-68465600	Transcr. at gene 5' and 3'	Hela-S3	cervix
6	chr5:68463800-68470800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:68463800-68484400	Weak transcription	Adipose Nuclei	Adipose
8	chr5:68463800-68484400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:68463800-68484400	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:68464000-68466800	Weak transcription	Right Ventricle	heart
11	chr5:68464000-68467000	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:68464000-68467200	Weak transcription	Brain Anterior Caudate	brain
13	chr5:68464000-68467400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:68464000-68468000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:68464000-68469000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:68464000-68470000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:68464000-68470000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:68464000-68470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:68464000-68470000	Weak transcription	Placenta	Placenta
20	chr5:68464000-68470000	Weak transcription	Spleen	Spleen
21	chr5:68464000-68470200	Weak transcription	Brain Substantia Nigra	brain
22	chr5:68464000-68470200	Weak transcription	Lung	lung
23	chr5:68464000-68470800	Weak transcription	Liver	Liver
24	chr5:68464000-68470800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr5:68464000-68471000	Weak transcription	Brain Angular Gyrus	brain
26	chr5:68464000-68472800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:68464000-68473000	Weak transcription	Esophagus	oesophagus
28	chr5:68464000-68473400	Weak transcription	Fetal Brain Male	brain
29	chr5:68464000-68475000	Weak transcription	Colonic Mucosa	Colon
30	chr5:68464000-68476200	Weak transcription	Stomach Mucosa	stomach
31	chr5:68464000-68478000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:68464000-68478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr5:68464000-68484400	Weak transcription	Pancreas	Pancrea
34	chr5:68464000-68484600	Weak transcription	Right Atrium	heart
35	chr5:68464200-68466800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:68464200-68467600	Weak transcription	Primary B cells from cord blood	blood
37	chr5:68464200-68467800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:68464200-68468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr5:68464200-68470000	Weak transcription	Gastric	stomach
40	chr5:68464200-68470800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr5:68464200-68470800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:68464200-68471000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr5:68464200-68474000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr5:68464200-68474000	Weak transcription	Small Intestine	intestine
45	chr5:68464200-68474600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:68464200-68484600	Weak transcription	Left Ventricle	heart
47	chr5:68464400-68465600	Genic enhancers	Fetal Thymus	thymus
48	chr5:68464400-68466400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:68464400-68467800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr5:68464400-68469200	Weak transcription	Primary B cells from peripheral blood	blood

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