Variant report

Variant	rs2561171
Chromosome Location	chr5:68681623-68681624
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68664076..68666329-chr5:68681503..68684780,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10036674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10037276	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10038816	0.81[EUR][1000 genomes]
rs10060524	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10068576	0.81[EUR][1000 genomes]
rs10072904	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10077413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168402	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168403	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168405	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168406	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168407	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168408	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168411	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1177557	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1183879	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1185246	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs182447	0.83[EUR][1000 genomes]
rs2434507	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439720	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2439722	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2561159	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2561160	0.82[EUR][1000 genomes]
rs2561172	0.81[EUR][1000 genomes]
rs2561182	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2561183	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2583699	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2583701	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28371924	0.80[EUR][1000 genomes]
rs28570129	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299072	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299073	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299074	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299076	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs299078	0.82[EUR][1000 genomes]
rs299079	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299080	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299081	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299082	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299083	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299084	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299085	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs299086	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299087	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299090	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299092	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299093	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299095	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299096	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299097	0.83[EUR][1000 genomes]
rs299101	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3797091	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55747363	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62371717	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450038	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7447816	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7448722	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730350	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7731269	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9686715	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2561171	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs2561171	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68666600-68689600	Weak transcription	Aorta	Aorta
2	chr5:68666600-68689800	Weak transcription	Gastric	stomach
3	chr5:68666600-68689800	Weak transcription	Right Ventricle	heart
4	chr5:68666600-68696200	Weak transcription	Pancreas	Pancrea
5	chr5:68666600-68705000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:68666600-68710800	Weak transcription	Esophagus	oesophagus
7	chr5:68666800-68710600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:68666800-68710600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:68666800-68710800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:68666800-68710800	Weak transcription	Psoas Muscle	Psoas
11	chr5:68667000-68684600	Weak transcription	Fetal Heart	heart
12	chr5:68667000-68690400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:68667200-68710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:68667200-68710800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:68667800-68710600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:68668000-68713000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:68668800-68683600	Weak transcription	Fetal Brain Male	brain
18	chr5:68668800-68712400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:68669200-68681800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr5:68669600-68697600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:68669600-68701200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:68669600-68702200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:68669600-68702800	Strong transcription	Liver	Liver
24	chr5:68669800-68697600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:68669800-68700400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:68669800-68700800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:68670200-68700800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:68670400-68683600	Strong transcription	Adipose Nuclei	Adipose
29	chr5:68670400-68697400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:68670400-68697600	Strong transcription	Fetal Thymus	thymus
31	chr5:68670600-68681800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:68670600-68702600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:68671200-68702400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:68672000-68681800	Strong transcription	Fetal Intestine Small	intestine
35	chr5:68672000-68683200	Weak transcription	Hela-S3	cervix
36	chr5:68672600-68685800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:68672600-68689600	Weak transcription	NHLF	lung
38	chr5:68672800-68685000	Weak transcription	Brain Angular Gyrus	brain
39	chr5:68673200-68688000	Weak transcription	Small Intestine	intestine
40	chr5:68673600-68692200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:68673800-68699800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:68674000-68699600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:68674200-68685400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:68674200-68702400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:68675000-68687000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:68675400-68705400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:68675600-68696000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:68675600-68708400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr5:68675800-68683000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:68675800-68696800	Weak transcription	HMEC	breast

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