Variant report

Variant	rs2549559
Chromosome Location	chr16:74563777-74563778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11640021	0.87[ASN][1000 genomes]
rs11641958	0.93[ASN][1000 genomes]
rs11644298	0.82[ASN][1000 genomes]
rs11648786	0.86[ASN][1000 genomes]
rs12446095	0.86[ASN][1000 genomes]
rs12449071	0.86[ASN][1000 genomes]
rs12598701	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12716768	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12927939	0.92[ASN][1000 genomes]
rs12930645	0.82[ASN][1000 genomes]
rs13339161	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13339456	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13380609	0.91[ASN][1000 genomes]
rs1469140	0.88[ASN][1000 genomes]
rs17672539	0.87[ASN][1000 genomes]
rs1971071	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2098754	0.87[ASN][1000 genomes]
rs2303281	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2549063	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2550816	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2868035	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28762730	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3096409	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3865164	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3960602	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3973385	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4404098	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4887772	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7188050	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7188197	0.86[ASN][1000 genomes]
rs7189123	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7190577	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7195020	0.85[AMR][1000 genomes]
rs7195196	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7195198	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8045653	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8053599	0.86[ASN][1000 genomes]
rs918782	0.87[ASN][1000 genomes]
rs9888755	0.84[AFR][1000 genomes]
rs9923616	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1065964	chr16:74088091-74575604	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	34 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv428806	chr16:74394226-74580125	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2549559	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs2549559	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs2549559	RFWD3	cis	Skin Sun Exposed Lower leg	GTEx
rs2549559	RFWD3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74525200-74565200	Weak transcription	Fetal Brain Male	brain
2	chr16:74525400-74572200	Weak transcription	HUVEC	blood vessel
3	chr16:74536000-74563800	Weak transcription	Fetal Kidney	kidney
4	chr16:74537400-74567000	Weak transcription	Colon Smooth Muscle	Colon
5	chr16:74537600-74565200	Weak transcription	Colonic Mucosa	Colon
6	chr16:74537600-74568600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr16:74537600-74579800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr16:74537600-74604800	Weak transcription	Thymus	Thymus
9	chr16:74537800-74568800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr16:74538000-74567000	Weak transcription	HMEC	breast
11	chr16:74538800-74566000	Weak transcription	NHEK	skin
12	chr16:74539000-74564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:74539200-74578200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr16:74539200-74581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr16:74539800-74565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:74540000-74579800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr16:74540800-74566400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr16:74542600-74567400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr16:74542600-74574800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr16:74542800-74566800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:74542800-74590400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr16:74543000-74567000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr16:74543000-74568000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr16:74543000-74570400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr16:74552200-74575400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr16:74552600-74580000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr16:74554600-74564400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr16:74555000-74582200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr16:74555400-74565600	Weak transcription	Hela-S3	cervix
30	chr16:74556000-74567600	Weak transcription	Fetal Muscle Leg	muscle
31	chr16:74556000-74572400	Weak transcription	Brain Angular Gyrus	brain
32	chr16:74556200-74564200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr16:74556200-74568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr16:74556400-74565600	Weak transcription	Brain Hippocampus Middle	brain
35	chr16:74556400-74567000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr16:74556400-74568600	Weak transcription	Brain Anterior Caudate	brain
37	chr16:74556400-74572400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr16:74556400-74595600	Weak transcription	NH-A	brain
39	chr16:74556800-74567000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr16:74556800-74567400	Weak transcription	Left Ventricle	heart
41	chr16:74556800-74568800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr16:74556800-74568800	Weak transcription	Brain Substantia Nigra	brain
43	chr16:74558200-74565400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr16:74558400-74568800	Weak transcription	Psoas Muscle	Psoas
45	chr16:74558800-74567400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:74558800-74578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr16:74559000-74566000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr16:74559000-74574600	Weak transcription	HepG2	liver
49	chr16:74559200-74564200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr16:74559200-74564200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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