Variant report

Variant	rs3851730
Chromosome Location	chr16:74485722-74485723
allele	C/T
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	chr16:74484837-74486178	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:74485563-74485738	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr16:74485014-74485849	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74483167..74486389-chr16:74491599..74494939,3	MCF-7	breast:
2	chr16:74484871..74487119-chr16:74488063..74490451,3	K562	blood:

Variant related genes	Relation type
RNU6-237P	TF binding region
ENSG00000260539	TF binding region
ENSG00000090863	Chromatin interaction
ENSG00000251794	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1019572	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10500587	0.85[ASN][1000 genomes]
rs11149722	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1132843	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639812	0.84[ASN][1000 genomes]
rs11643293	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11647149	1.00[ASN][1000 genomes]
rs12325017	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12446054	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12447531	0.82[ASN][1000 genomes]
rs12449125	0.80[ASN][1000 genomes]
rs13359	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985611	0.80[ASN][1000 genomes]
rs2288053	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2303278	0.84[ASN][1000 genomes]
rs3785312	0.86[ASN][1000 genomes]
rs3826239	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3851729	0.88[AFR][1000 genomes]
rs4888238	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4888240	0.93[ASN][1000 genomes]
rs4888242	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6564117	0.83[ASN][1000 genomes]
rs7978	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv1066212	chr16:74068470-74527133	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv542954	chr16:74068470-74527133	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv833277	chr16:74334787-74498133	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	esv2762054	chr16:74337036-74507056	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1817585	chr16:74355081-74486997	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
11	esv1829589	chr16:74366364-74496761	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	nsv960357	chr16:74480805-74507776	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	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
17	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3851730	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs3851730	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs3851730	RFWD3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74468200-74498400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:74471000-74485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr16:74473000-74486800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr16:74473000-74487000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr16:74474000-74485800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr16:74475400-74486800	Weak transcription	Fetal Kidney	kidney
7	chr16:74479800-74489400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr16:74480000-74486200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:74480000-74488200	Strong transcription	Primary T cells from cord blood	blood
10	chr16:74480400-74501000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:74480400-74501400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr16:74480400-74502600	Strong transcription	Thymus	Thymus
13	chr16:74480400-74530800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr16:74480400-74530800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr16:74480400-74531800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr16:74480600-74492800	Strong transcription	Brain Germinal Matrix	brain
17	chr16:74480600-74500200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr16:74480600-74503000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:74480600-74530600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr16:74480800-74486400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr16:74480800-74500400	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr16:74480800-74530600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr16:74480800-74530800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:74481200-74520000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr16:74481200-74520200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr16:74481400-74487800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr16:74481600-74487000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr16:74481800-74487200	Strong transcription	Fetal Lung	lung
29	chr16:74481800-74487600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr16:74481800-74487600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr16:74481800-74492000	Strong transcription	Fetal Brain Female	brain
32	chr16:74481800-74519800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr16:74482000-74487600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr16:74482000-74514600	Strong transcription	Fetal Thymus	thymus
35	chr16:74482200-74487800	Strong transcription	Brain Hippocampus Middle	brain
36	chr16:74482600-74486000	Enhancers	Esophagus	oesophagus
37	chr16:74483000-74486000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr16:74483000-74487600	Strong transcription	Primary B cells from cord blood	blood
39	chr16:74483000-74530600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr16:74483000-74530800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:74483200-74494600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr16:74483200-74520000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr16:74483200-74520400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr16:74483400-74492000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr16:74483600-74486000	Strong transcription	GM12878-XiMat	blood
46	chr16:74483600-74487600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr16:74483600-74487600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr16:74483800-74486600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:74483800-74486600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr16:74483800-74487400	Strong transcription	Brain Anterior Caudate	brain

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