Variant report

Variant	rs10038816
Chromosome Location	chr5:68674060-68674061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68665185..68668152-chr5:68673816..68676048,2	MCF-7	breast:
2	chr5:68665954..68668664-chr5:68673852..68678917,5	K562	blood:

Variant related genes	Relation type
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10035835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10036674	0.81[EUR][1000 genomes]
rs10044508	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10064264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10068576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077413	0.81[EUR][1000 genomes]
rs10077458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10471774	0.85[AFR][1000 genomes]
rs1168404	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168410	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1177556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1183278	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2561169	0.86[EUR][1000 genomes]
rs2561171	0.81[EUR][1000 genomes]
rs2561172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28703034	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs299075	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs299077	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs299084	0.81[EUR][1000 genomes]
rs299088	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs299094	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299098	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs299099	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299102	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4252228	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62373187	0.85[AFR][1000 genomes]
rs7448722	0.81[EUR][1000 genomes]
rs7712318	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3425236	chr5:68672546-68674544	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10038816	CCDC125	cis	lung	GTEx
rs10038816	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs10038816	MRPS36	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68666200-68678000	Weak transcription	Spleen	Spleen
2	chr5:68666600-68677800	Weak transcription	Colonic Mucosa	Colon
3	chr5:68666600-68677800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:68666600-68681000	Weak transcription	Lung	lung
5	chr5:68666600-68689600	Weak transcription	Aorta	Aorta
6	chr5:68666600-68689800	Weak transcription	Gastric	stomach
7	chr5:68666600-68689800	Weak transcription	Right Ventricle	heart
8	chr5:68666600-68696200	Weak transcription	Pancreas	Pancrea
9	chr5:68666600-68705000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:68666600-68710800	Weak transcription	Esophagus	oesophagus
11	chr5:68666800-68676600	Weak transcription	Thymus	Thymus
12	chr5:68666800-68677800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:68666800-68677800	Weak transcription	Fetal Kidney	kidney
14	chr5:68666800-68710600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:68666800-68710600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:68666800-68710800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:68666800-68710800	Weak transcription	Psoas Muscle	Psoas
18	chr5:68667000-68674400	Weak transcription	HMEC	breast
19	chr5:68667000-68677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:68667000-68684600	Weak transcription	Fetal Heart	heart
21	chr5:68667000-68690400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:68667200-68710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:68667200-68710800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:68667800-68674200	Weak transcription	A549	lung
25	chr5:68667800-68677800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:68667800-68679600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:68667800-68710600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:68668000-68713000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:68668200-68674200	Weak transcription	Brain Anterior Caudate	brain
30	chr5:68668800-68683600	Weak transcription	Fetal Brain Male	brain
31	chr5:68668800-68712400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:68669200-68681800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr5:68669600-68674800	Strong transcription	Placenta	Placenta
34	chr5:68669600-68674800	Strong transcription	Dnd41	blood
35	chr5:68669600-68675000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:68669600-68675000	Strong transcription	Osteobl	bone
37	chr5:68669600-68675200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr5:68669600-68697600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:68669600-68701200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:68669600-68702200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:68669600-68702800	Strong transcription	Liver	Liver
42	chr5:68669800-68674200	Strong transcription	NHEK	skin
43	chr5:68669800-68674800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:68669800-68676200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:68669800-68678400	Strong transcription	NHDF-Ad	bronchial
46	chr5:68669800-68697600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:68669800-68700400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:68669800-68700800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr5:68670000-68674800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:68670000-68674800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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