Variant report

Variant	rs9888968
Chromosome Location	chr16:74580510-74580511
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	chr16:74579440..74581506-chr16:74639502..74641032,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10468356	0.84[ASN][1000 genomes]
rs12445991	0.86[ASN][1000 genomes]
rs12448026	0.85[ASN][1000 genomes]
rs1820262	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2550824	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3923201	0.90[ASN][1000 genomes]
rs4600490	0.87[ASN][1000 genomes]
rs4888253	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4888256	0.82[ASN][1000 genomes]
rs55960814	0.86[ASN][1000 genomes]
rs62054177	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6564141	0.86[ASN][1000 genomes]
rs6564142	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67414268	0.82[ASN][1000 genomes]
rs71392603	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7185026	0.87[ASN][1000 genomes]
rs7201105	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7203452	0.87[ASN][1000 genomes]
rs7205813	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7359390	0.86[ASN][1000 genomes]
rs8046158	0.82[ASN][1000 genomes]
rs8047243	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8048239	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8049138	0.87[ASN][1000 genomes]
rs8050668	0.90[ASN][1000 genomes]
rs8050850	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8051990	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8052389	0.84[ASN][1000 genomes]
rs8053369	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8055380	0.85[ASN][1000 genomes]
rs8055803	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8056718	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8058256	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8058692	0.91[ASN][1000 genomes]
rs8062404	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9888950	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9888976	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9923644	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9929933	0.87[ASN][1000 genomes]
rs9930003	0.92[ASN][1000 genomes]
rs9932735	0.82[ASN][1000 genomes]
rs9936239	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9938859	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
3	esv2758431	chr16:74334780-74587185	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2758656	chr16:74334780-74587185	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv833278	chr16:74415944-74584123	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv1060629	chr16:74483574-74660669	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv833279	chr16:74490746-74663073	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
11	nsv906905	chr16:74527618-74679244	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9888968	RFWD3	cis	Thyroid	GTEx
rs9888968	RFWD3	cis	Skin Sun Exposed Lower leg	GTEx
rs9888968	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs9888968	RFWD3	cis	Esophagus Mucosa	GTEx
rs9888968	RFWD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74537600-74604800	Weak transcription	Thymus	Thymus
2	chr16:74539200-74581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr16:74542800-74590400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr16:74555000-74582200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr16:74556400-74595600	Weak transcription	NH-A	brain
6	chr16:74559200-74594000	Weak transcription	Ovary	ovary
7	chr16:74559400-74591200	Weak transcription	Primary T cells from cord blood	blood
8	chr16:74563200-74598000	Weak transcription	Fetal Intestine Small	intestine
9	chr16:74563200-74622400	Weak transcription	Fetal Stomach	stomach
10	chr16:74565000-74597000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:74565600-74597000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr16:74569000-74581600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr16:74569600-74581800	Weak transcription	Psoas Muscle	Psoas
14	chr16:74575200-74580800	Weak transcription	K562	blood
15	chr16:74578400-74591200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr16:74578600-74582200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr16:74578600-74587600	Weak transcription	HUVEC	blood vessel
18	chr16:74578600-74589800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr16:74578600-74597400	Weak transcription	Pancreas	Pancrea
20	chr16:74579200-74597200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr16:74579400-74581000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr16:74579800-74581000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr16:74580000-74580600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr16:74580200-74580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr16:74580200-74581600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr16:74580200-74591400	Weak transcription	HepG2	liver
27	chr16:74580200-74593400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr16:74580400-74591200	Weak transcription	Primary T cells fromperipheralblood	blood

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