Variant report

Variant	rs390169
Chromosome Location	chr5:68469687-68469688
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68467066..68470056-chr5:68482970..68485828,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153044	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs100192	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11742461	0.81[ASN][1000 genomes]
rs11744596	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11745578	0.81[ASN][1000 genomes]
rs12659146	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13175606	0.80[ASN][1000 genomes]
rs151589	0.80[ASN][1000 genomes]
rs163442	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs163443	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs163444	0.80[ASN][1000 genomes]
rs164386	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164388	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs164389	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164390	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164715	0.80[ASN][1000 genomes]
rs1683831	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs184747	0.80[ASN][1000 genomes]
rs2002825	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242351	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs239591	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2637128	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2637129	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28506805	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28576332	0.81[ASN][1000 genomes]
rs28693971	0.81[ASN][1000 genomes]
rs2913707	0.80[ASN][1000 genomes]
rs2930944	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2930946	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932770	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932771	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932777	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932778	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932780	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932783	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972358	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972373	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972374	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972390	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34845020	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs350093	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs350094	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs350095	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350099	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350105	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs350107	0.80[ASN][1000 genomes]
rs350115	0.80[ASN][1000 genomes]
rs350119	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350120	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350124	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350125	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs352626	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs375285	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs376768	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs379434	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs386640	0.80[ASN][1000 genomes]
rs389686	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs389938	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs395122	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs419902	0.80[ASN][1000 genomes]
rs437665	0.89[ASN][1000 genomes]
rs444305	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs476125	0.89[ASN][1000 genomes]
rs4976159	0.82[ASN][1000 genomes]
rs4976188	0.82[ASN][1000 genomes]
rs648489	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6862253	0.80[ASN][1000 genomes]
rs693725	0.80[ASN][1000 genomes]
rs7719040	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs875459	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs390169	CDK7	cis	Muscle Skeletal	GTEx
rs390169	CCDC125	cis	Muscle Skeletal	GTEx
rs390169	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

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	chr5:68464400-68470600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:68464400-68470800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:68464400-68471000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:68464400-68473200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:68464400-68473200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:68464400-68473600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:68464400-68479000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:68464400-68484400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:68464600-68470000	Weak transcription	Fetal Brain Female	brain
42	chr5:68464600-68470800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:68464600-68473600	Strong transcription	Fetal Muscle Leg	muscle
44	chr5:68464600-68484400	Weak transcription	HSMMtube	muscle
45	chr5:68464800-68474000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr5:68464800-68474400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:68464800-68474400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:68464800-68474600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr5:68464800-68474600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:68464800-68474600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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