Variant report

Variant	rs6884416
Chromosome Location	chr5:154231779-154231780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:154231765-154231866	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:154231167..154234923-chr5:154237535..154239823,3	K562	blood:
2	chr5:154229420..154232188-chr5:154319617..154321370,2	K562	blood:
3	chr5:154228281..154231986-chr5:154234217..154239374,12	MCF-7	breast:

Variant related genes	Relation type
FAXDC2	TF binding region
ENSG00000082515	Chromatin interaction
ENSG00000170271	Chromatin interaction
ENSG00000155508	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1035368	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11167705	0.84[ASN][1000 genomes]
rs12188828	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12300	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs164195	0.85[EUR][1000 genomes]
rs17116411	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116414	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116421	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116442	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116534	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs180846	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs186971	0.89[EUR][1000 genomes]
rs1974776	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1974777	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2042168	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2112223	0.94[EUR][1000 genomes]
rs2161128	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2258437	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2396999	0.83[EUR][1000 genomes]
rs2431184	0.92[ASN][1000 genomes]
rs2544859	0.89[EUR][1000 genomes]
rs2544860	0.84[ASN][1000 genomes]
rs2544866	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544874	0.97[EUR][1000 genomes]
rs2544875	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544876	0.97[EUR][1000 genomes]
rs2544880	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544884	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs255529	0.86[ASN][1000 genomes]
rs2560063	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2644743	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2644744	0.94[EUR][1000 genomes]
rs2644746	0.92[EUR][1000 genomes]
rs2688186	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688187	0.97[EUR][1000 genomes]
rs2688188	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688189	0.97[EUR][1000 genomes]
rs2688190	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2688191	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688193	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688194	0.83[EUR][1000 genomes]
rs2688195	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688198	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2688199	0.95[EUR][1000 genomes]
rs2688200	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688201	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688206	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2688208	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs348739	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348748	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs348749	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs348750	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348751	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348752	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348754	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39614	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4354100	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs454161	0.92[ASN][1000 genomes]
rs4958771	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55770418	0.92[EUR][1000 genomes]
rs56374414	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58415346	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59525998	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59749917	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580122	0.82[ASN][1000 genomes]
rs6879277	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs702742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276742	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73280705	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7723269	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7728194	0.84[EUR][1000 genomes]
rs816717	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816718	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816720	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816722	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816734	0.88[ASN][1000 genomes]
rs816743	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816747	0.82[ASN][1000 genomes]
rs888694	0.85[EUR][1000 genomes]
rs960499	0.82[ASN][1000 genomes]
rs9942412	0.84[AMR][1000 genomes];0.84[EUR][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	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154211400-154235800	Weak transcription	Dnd41	blood
2	chr5:154214800-154236400	Weak transcription	GM12878-XiMat	blood
3	chr5:154215200-154236400	Weak transcription	A549	lung
4	chr5:154219000-154236600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:154230200-154236400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:154230200-154236400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:154230200-154236800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:154230400-154235400	Weak transcription	Placenta	Placenta
9	chr5:154230400-154235600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:154230600-154235400	Weak transcription	Fetal Brain Male	brain
11	chr5:154230600-154236400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:154230600-154236600	Weak transcription	Primary B cells from cord blood	blood
13	chr5:154230600-154236600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:154230800-154232200	Enhancers	Colon Smooth Muscle	Colon
15	chr5:154230800-154236200	Weak transcription	Fetal Intestine Small	intestine
16	chr5:154230800-154236200	Weak transcription	Fetal Thymus	thymus
17	chr5:154230800-154236400	Weak transcription	Fetal Brain Female	brain
18	chr5:154230800-154236400	Weak transcription	HMEC	breast
19	chr5:154230800-154236400	Weak transcription	HUVEC	blood vessel
20	chr5:154230800-154236400	Weak transcription	NH-A	brain
21	chr5:154230800-154236400	Weak transcription	NHEK	skin
22	chr5:154230800-154236600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:154230800-154236600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:154230800-154236600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:154230800-154236600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:154230800-154236600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:154230800-154236600	Weak transcription	Aorta	Aorta
28	chr5:154230800-154236600	Weak transcription	Colonic Mucosa	Colon
29	chr5:154230800-154236600	Weak transcription	Fetal Intestine Large	intestine
30	chr5:154231000-154235400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:154231000-154236200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr5:154231000-154236200	Weak transcription	Fetal Lung	lung
33	chr5:154231000-154236400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:154231000-154236400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:154231000-154236400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:154231000-154236400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:154231000-154236400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:154231000-154236400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:154231000-154236400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:154231000-154236400	Weak transcription	Right Ventricle	heart
41	chr5:154231000-154236400	Weak transcription	HSMM	muscle
42	chr5:154231000-154236400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr5:154231000-154236600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:154231000-154236600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:154231000-154236600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr5:154231000-154236600	Weak transcription	Primary T cells from cord blood	blood
47	chr5:154231200-154235200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr5:154231200-154235200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:154231200-154235200	Weak transcription	K562	blood
50	chr5:154231200-154235600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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