Variant report

Variant	rs250439
Chromosome Location	chr5:14685762-14685763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:14680587..14682687-chr5:14683791..14686120,3	K562	blood:
2	chr5:14685519..14686385-chr5:15013737..15014695,6	MCF-7	breast:
3	chr5:14680121..14683231-chr5:14683255..14687909,6	K562	blood:
4	chr5:14670223..14672828-chr5:14683390..14686379,2	K562	blood:
5	chr5:14663633..14666342-chr5:14685335..14688986,4	K562	blood:
6	chr5:14683758..14686068-chr5:14687921..14690777,3	K562	blood:
7	chr5:14685514..14686500-chr5:15003255..15004071,2	MCF-7	breast:
8	chr5:14685322..14687229-chr5:14691239..14694070,2	MCF-7	breast:
9	chr5:14676057..14679140-chr5:14685334..14687746,3	K562	blood:
10	chr5:14684890..14686885-chr5:14687284..14690002,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000154124	Chromatin interaction
ENSG00000261360	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs13189930	0.87[EUR][1000 genomes]
rs149493	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149617	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875513	0.92[ASN][1000 genomes]
rs250440	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs258290	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs258374	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs25945	0.84[ASN][1000 genomes]
rs25951	0.84[ASN][1000 genomes]
rs25952	0.85[ASN][1000 genomes]
rs25983	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs25992	0.81[ASN][1000 genomes]
rs26307	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27356	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs27882	0.84[ASN][1000 genomes]
rs27911	0.81[ASN][1000 genomes]
rs28004	0.84[ASN][1000 genomes]
rs31919	0.85[ASN][1000 genomes]
rs31920	0.84[ASN][1000 genomes]
rs31921	0.84[ASN][1000 genomes]
rs31922	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs31923	0.85[ASN][1000 genomes]
rs31925	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs31926	0.84[ASN][1000 genomes]
rs31928	0.84[ASN][1000 genomes]
rs31929	0.84[ASN][1000 genomes]
rs31930	0.84[ASN][1000 genomes]
rs31968	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853119	0.87[ASN][1000 genomes]
rs3866215	0.90[ASN][1000 genomes]
rs40578	0.85[ASN][1000 genomes]
rs42358	0.84[ASN][1000 genomes]
rs42410	0.84[ASN][1000 genomes]
rs42681	0.83[ASN][1000 genomes]
rs4702043	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6872954	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs250439	FAM105B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14666400-14688200	Weak transcription	Ovary	ovary
2	chr5:14666600-14688200	Weak transcription	Brain Germinal Matrix	brain
3	chr5:14667000-14690400	Weak transcription	Fetal Brain Male	brain
4	chr5:14672200-14690400	Strong transcription	Hela-S3	cervix
5	chr5:14673800-14690000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:14674000-14712800	Strong transcription	Fetal Intestine Large	intestine
7	chr5:14674600-14687200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:14674600-14688400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:14674600-14695600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:14675200-14695800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:14676800-14687800	Weak transcription	Fetal Kidney	kidney
12	chr5:14676800-14690600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:14676800-14705600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:14677000-14685800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:14677000-14688400	Weak transcription	Stomach Mucosa	stomach
16	chr5:14677000-14695200	Strong transcription	K562	blood
17	chr5:14677600-14689800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:14677600-14705600	Strong transcription	Dnd41	blood
19	chr5:14677800-14685800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr5:14677800-14704000	Strong transcription	HepG2	liver
21	chr5:14678000-14686000	Strong transcription	Primary T cells from cord blood	blood
22	chr5:14678000-14689800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:14678000-14690200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr5:14678000-14690200	Strong transcription	Primary B cells from cord blood	blood
25	chr5:14678200-14685800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:14678200-14685800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:14678200-14689200	Strong transcription	Fetal Intestine Small	intestine
28	chr5:14678200-14690400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:14678200-14690400	Strong transcription	Fetal Stomach	stomach
30	chr5:14678400-14685800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:14678600-14685800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr5:14678600-14704200	Strong transcription	Fetal Thymus	thymus
33	chr5:14678800-14686000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr5:14679200-14689600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:14679400-14685800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr5:14679600-14686600	Weak transcription	NH-A	brain
37	chr5:14680400-14685800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:14680400-14688400	Strong transcription	Lung	lung
39	chr5:14680800-14685800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr5:14680800-14685800	Strong transcription	GM12878-XiMat	blood
41	chr5:14680800-14687200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:14680800-14687200	Weak transcription	Right Atrium	heart
43	chr5:14682000-14687400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr5:14682600-14685800	Weak transcription	Fetal Brain Female	brain
45	chr5:14682800-14686800	Weak transcription	Small Intestine	intestine
46	chr5:14682800-14687600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:14683200-14685800	Weak transcription	NHEK	skin
48	chr5:14683200-14687200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:14683200-14688200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr5:14683400-14686600	Weak transcription	Muscle Satellite Cultured Cells	--

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