Variant report

Variant	rs12651858
Chromosome Location	chr5:68577467-68577468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68577265..68579159-chr5:68664266..68665815,2	K562	blood:
2	chr5:68572340..68574718-chr5:68576377..68579078,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF9-3	chr5:68577172-68578861	NONHSAT101908

Variant related genes	Relation type
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10940206	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12652124	0.85[ASN][1000 genomes]
rs12656423	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12656449	1.00[EUR][1000 genomes]
rs12656918	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12657418	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2054977	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs338685	0.93[JPT][hapmap]
rs3934529	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443380	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4976158	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59515371	1.00[EUR][1000 genomes]
rs60113639	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60824482	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73125214	0.87[EUR][1000 genomes]
rs73125295	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73127319	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73127323	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73127331	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7733529	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12651858	CCDC125	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
4	chr5:68546200-68579200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:68549400-68577600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:68549600-68577600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:68550400-68581800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:68552000-68581200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:68552200-68580800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:68552200-68588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:68553000-68581400	Weak transcription	Psoas Muscle	Psoas
12	chr5:68553800-68587800	Weak transcription	Colonic Mucosa	Colon
13	chr5:68554000-68577600	Weak transcription	Fetal Heart	heart
14	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:68559000-68583400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:68559200-68581200	Weak transcription	Fetal Kidney	kidney
17	chr5:68559600-68584000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:68562600-68578800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:68562600-68584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:68563000-68585200	Strong transcription	Liver	Liver
21	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
22	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:68566000-68591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:68567800-68578200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:68569400-68582000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:68570200-68578200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:68570800-68578800	Strong transcription	Adipose Nuclei	Adipose
29	chr5:68571400-68578200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:68571600-68578400	Strong transcription	Fetal Stomach	stomach
31	chr5:68571600-68579000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:68571600-68579800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr5:68571600-68581600	Strong transcription	Fetal Thymus	thymus
34	chr5:68572000-68578000	Strong transcription	Placenta	Placenta
35	chr5:68573000-68587800	Weak transcription	Hela-S3	cervix
36	chr5:68573000-68590600	Weak transcription	HUVEC	blood vessel
37	chr5:68573200-68585600	Strong transcription	Fetal Intestine Small	intestine
38	chr5:68573400-68578000	Strong transcription	Osteobl	bone
39	chr5:68573400-68578200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:68573600-68578000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:68573800-68580400	Weak transcription	NHDF-Ad	bronchial
42	chr5:68574000-68585000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:68574400-68577600	Strong transcription	Brain Hippocampus Middle	brain
44	chr5:68574400-68577600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr5:68574600-68577800	Strong transcription	NH-A	brain
46	chr5:68574600-68578000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:68574600-68578000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:68574800-68577600	Strong transcription	NHLF	lung
49	chr5:68574800-68581200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:68575000-68577600	Strong transcription	NHEK	skin

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