Variant report

Variant	rs350120
Chromosome Location	chr5:68476581-68476582
allele	A/G
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	chr5:68476203-68476619	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68472735..68477267-chr5:68482092..68486946,8	MCF-7	breast:
2	chr5:68463301..68465130-chr5:68476296..68477877,2	MCF-7	breast:
3	chr5:68473378..68475599-chr5:68475846..68477931,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238334	TF binding region
ENSG00000153044	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs100192	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742461	0.87[ASN][1000 genomes]
rs11744596	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11745578	0.87[ASN][1000 genomes]
rs12659146	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13175606	0.85[ASN][1000 genomes]
rs151589	0.85[ASN][1000 genomes]
rs163442	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs163443	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs163444	0.85[ASN][1000 genomes]
rs164386	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164388	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs164389	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164390	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164715	0.85[ASN][1000 genomes]
rs1650779	0.81[ASN][1000 genomes]
rs1683831	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs184747	0.85[ASN][1000 genomes]
rs2002825	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242351	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239591	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2450230	0.81[ASN][1000 genomes]
rs2637128	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2637129	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28506805	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28576332	0.87[ASN][1000 genomes]
rs28693971	0.87[ASN][1000 genomes]
rs2913707	0.84[ASN][1000 genomes]
rs2930944	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930945	0.82[ASN][1000 genomes]
rs2930946	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932770	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932771	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932772	0.83[ASN][1000 genomes]
rs2932773	0.83[ASN][1000 genomes]
rs2932775	0.83[ASN][1000 genomes]
rs2932776	0.83[ASN][1000 genomes]
rs2932777	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932778	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932780	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932783	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972358	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972373	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972374	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972390	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34845020	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350093	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350094	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs350095	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350099	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350105	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350107	0.85[ASN][1000 genomes]
rs350109	0.84[ASN][1000 genomes]
rs350115	0.85[ASN][1000 genomes]
rs350119	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350123	0.83[ASN][1000 genomes]
rs350124	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350125	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs351424	0.81[ASN][1000 genomes]
rs352626	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353656	0.83[ASN][1000 genomes]
rs375285	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376768	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs379106	0.81[ASN][1000 genomes]
rs379434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs386640	0.85[ASN][1000 genomes]
rs389686	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs389938	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs390169	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs395122	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419902	0.85[ASN][1000 genomes]
rs437665	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs444305	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs476125	0.93[ASN][1000 genomes]
rs4976159	0.88[ASN][1000 genomes]
rs4976188	0.88[ASN][1000 genomes]
rs648489	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651076	0.80[ASN][1000 genomes]
rs6862253	0.87[ASN][1000 genomes]
rs693725	0.85[ASN][1000 genomes]
rs7719040	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875459	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs350120	CCDC125	cis	Muscle Skeletal	GTEx
rs350120	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs350120	CDK7	cis	Muscle Skeletal	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68463800-68484400	Weak transcription	Adipose Nuclei	Adipose
2	chr5:68463800-68484400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:68463800-68484400	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:68464000-68478000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:68464000-68478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:68464000-68484400	Weak transcription	Pancreas	Pancrea
7	chr5:68464000-68484600	Weak transcription	Right Atrium	heart
8	chr5:68464200-68484600	Weak transcription	Left Ventricle	heart
9	chr5:68464400-68479000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:68464400-68484400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:68464600-68484400	Weak transcription	HSMMtube	muscle
12	chr5:68466800-68484400	Weak transcription	Fetal Heart	heart
13	chr5:68468000-68484400	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:68468000-68484400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:68468400-68484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:68470600-68484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:68471200-68476600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:68471200-68477200	Weak transcription	HepG2	liver
19	chr5:68471200-68484400	Weak transcription	Brain Anterior Caudate	brain
20	chr5:68471200-68484400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:68471200-68484600	Weak transcription	Primary T cells from cord blood	blood
22	chr5:68471200-68484600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:68471400-68477800	Weak transcription	Gastric	stomach
24	chr5:68471400-68484400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:68471400-68484400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:68471400-68484600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:68471400-68484600	Weak transcription	Liver	Liver
28	chr5:68471400-68484600	Weak transcription	Brain Substantia Nigra	brain
29	chr5:68471400-68484600	Weak transcription	Spleen	Spleen
30	chr5:68471600-68476600	Weak transcription	Fetal Brain Female	brain
31	chr5:68471600-68484200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:68471600-68484400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:68471600-68484400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:68471600-68484600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:68471600-68484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:68472000-68484400	Weak transcription	Fetal Intestine Large	intestine
37	chr5:68472000-68484600	Weak transcription	Ovary	ovary
38	chr5:68472200-68479200	Weak transcription	Fetal Kidney	kidney
39	chr5:68472200-68479600	Weak transcription	Brain Angular Gyrus	brain
40	chr5:68472200-68484400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:68472200-68484400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:68472200-68484400	Weak transcription	NHLF	lung
43	chr5:68472200-68484600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:68472400-68484400	Weak transcription	Fetal Intestine Small	intestine
45	chr5:68472400-68484600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:68472800-68484400	Weak transcription	Fetal Stomach	stomach
47	chr5:68473400-68484200	Weak transcription	Placenta	Placenta
48	chr5:68473400-68484400	Weak transcription	GM12878-XiMat	blood
49	chr5:68473400-68484600	Weak transcription	Thymus	Thymus
50	chr5:68473600-68477000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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