Variant report

Variant	rs56099065
Chromosome Location	chr16:74696959-74696960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:74696896-74698252	K562	blood:	n/a	n/a
2	POLR2A	chr16:74696942-74698375	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:74696901-74698428	K562	blood:	n/a	n/a
4	POLR2A	chr16:74696926-74698005	K562	blood:	n/a	n/a
5	POLR2A	chr16:74696933-74697126	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr16:74696902-74697514	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:74657630..74659377-chr16:74696166..74698749,2	K562	blood:
2	chr16:74695152..74698756-chr16:74699147..74702582,8	MCF-7	breast:
3	chr16:74660349..74663096-chr16:74695955..74699046,3	MCF-7	breast:
4	chr16:74695853..74699155-chr16:74725334..74728139,3	K562	blood:
5	chr16:74696101..74698353-chr16:74734070..74735926,3	MCF-7	breast:
6	chr16:74696660..74698219-chr16:74749550..74751165,2	K562	blood:
7	chr16:74639132..74641827-chr16:74694832..74697814,3	MCF-7	breast:
8	chr16:74691160..74693410-chr16:74694917..74697832,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000262904	TF binding region
ENSG00000168404	Chromatin interaction
ENSG00000090863	Chromatin interaction
ENSG00000103089	Chromatin interaction
ENSG00000262904	Chromatin interaction
ENSG00000168411	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs28681530	0.83[AMR][1000 genomes]
rs4072222	0.82[AMR][1000 genomes]
rs4888262	0.81[AMR][1000 genomes]
rs4888265	0.81[AMR][1000 genomes]
rs4888267	0.85[AMR][1000 genomes]
rs4888274	0.82[AMR][1000 genomes]
rs57488599	0.83[AMR][1000 genomes]
rs7191665	0.85[AMR][1000 genomes]
rs7201320	0.87[AMR][1000 genomes]
rs8052367	0.81[AMR][1000 genomes]
rs8058133	0.81[AMR][1000 genomes]
rs8061942	0.86[AMR][1000 genomes]
rs8062783	0.87[AMR][1000 genomes]
rs9923145	0.85[AMR][1000 genomes]
rs9931225	0.86[AMR][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	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
2	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
3	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
4	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
5	esv275138	chr16:74647795-74722907	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv2760414	chr16:74647795-74741615	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	67 gene(s)	inside rSNPs	diseases
8	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
9	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
10	nsv572975	chr16:74677312-74702254	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56099065	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs56099065	MLKL	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74652200-74699000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:74653200-74698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:74653400-74699000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr16:74656800-74699400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:74657000-74699200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:74657200-74699400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr16:74657200-74699600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr16:74657400-74699200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:74657400-74699600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr16:74658200-74697200	Weak transcription	Fetal Brain Male	brain
11	chr16:74678600-74699800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr16:74685000-74700000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr16:74685800-74699400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr16:74687200-74699800	Weak transcription	Right Atrium	heart
15	chr16:74688000-74699200	Strong transcription	Placenta	Placenta
16	chr16:74688000-74699400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr16:74689000-74698800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr16:74689200-74699600	Strong transcription	Fetal Intestine Small	intestine
19	chr16:74689200-74699800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr16:74689400-74699200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr16:74689600-74699200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr16:74689800-74699600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr16:74690000-74699400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr16:74690200-74699000	Strong transcription	Fetal Brain Female	brain
25	chr16:74690400-74698200	Strong transcription	Primary hematopoietic stem cells	blood
26	chr16:74690600-74698200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr16:74690600-74698800	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr16:74690600-74699000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:74690600-74699000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr16:74690800-74699000	Strong transcription	Osteobl	bone
31	chr16:74691600-74699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr16:74691600-74699200	Strong transcription	Fetal Lung	lung
33	chr16:74691600-74699200	Strong transcription	NH-A	brain
34	chr16:74691800-74698000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr16:74692000-74697400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr16:74692000-74698000	Strong transcription	HSMM	muscle
37	chr16:74692000-74698200	Strong transcription	Brain Hippocampus Middle	brain
38	chr16:74692000-74699200	Strong transcription	Ovary	ovary
39	chr16:74692000-74699200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr16:74692000-74699400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr16:74692200-74699200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr16:74692400-74698800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr16:74692400-74698800	Strong transcription	Lung	lung
44	chr16:74692400-74698800	Strong transcription	HUVEC	blood vessel
45	chr16:74692400-74699000	Strong transcription	Adipose Nuclei	Adipose
46	chr16:74692400-74699800	Weak transcription	Stomach Mucosa	stomach
47	chr16:74692600-74697000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr16:74692600-74699000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr16:74692600-74699000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:74692600-74699000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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