Variant report

Variant	rs4887778
Chromosome Location	chr16:74638159-74638160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74622797..74625662-chr16:74635267..74638190,2	K562	blood:
2	chr16:74637522..74639307-chr16:74639433..74640969,2	K562	blood:
3	chr16:74619421..74621291-chr16:74638015..74640531,2	MCF-7	breast:
4	chr16:74624724..74627496-chr16:74637454..74640972,3	MCF-7	breast:
5	chr16:74635090..74638243-chr16:74699211..74701869,3	K562	blood:

Variant related genes	Relation type
ENSG00000262904	Chromatin interaction
ENSG00000168411	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11149758	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11640231	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12600208	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2078330	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap]
rs28417898	0.83[EUR][1000 genomes]
rs3815826	0.81[GIH][hapmap]
rs4334322	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4462622	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4888272	0.82[CEU][hapmap]
rs56283458	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62051923	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62051924	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8047350	0.85[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4887778	RFWD3	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74605200-74639800	Weak transcription	Esophagus	oesophagus
2	chr16:74608400-74638200	Weak transcription	Fetal Brain Female	brain
3	chr16:74612000-74638600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr16:74618000-74638400	Weak transcription	Brain Substantia Nigra	brain
5	chr16:74624200-74638600	Weak transcription	Placenta	Placenta
6	chr16:74624200-74639200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr16:74628000-74638800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:74628600-74638200	Weak transcription	Colonic Mucosa	Colon
9	chr16:74630800-74638600	Weak transcription	Right Ventricle	heart
10	chr16:74631200-74639800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:74632200-74638600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr16:74632200-74638600	Weak transcription	Fetal Muscle Leg	muscle
13	chr16:74632200-74638800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr16:74632600-74639200	Weak transcription	Fetal Intestine Small	intestine
15	chr16:74634400-74638200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:74634600-74640200	Weak transcription	Spleen	Spleen
17	chr16:74635000-74639200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr16:74635400-74638600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr16:74635600-74638400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr16:74635800-74638200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr16:74635800-74638600	Weak transcription	Thymus	Thymus
22	chr16:74635800-74639000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr16:74635800-74639200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr16:74635800-74639200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr16:74635800-74639200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr16:74635800-74639200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr16:74635800-74639200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr16:74636000-74638200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr16:74636000-74638200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr16:74636000-74638200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr16:74636000-74638200	Weak transcription	Fetal Lung	lung
32	chr16:74636000-74638400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr16:74636000-74639200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr16:74636000-74639200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr16:74636000-74639200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr16:74636000-74639200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr16:74636200-74639200	Weak transcription	Stomach Mucosa	stomach
38	chr16:74636200-74640000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr16:74636400-74639200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr16:74636800-74638800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:74636800-74639000	Enhancers	Left Ventricle	heart
42	chr16:74636800-74639000	Enhancers	Psoas Muscle	Psoas
43	chr16:74636800-74639200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr16:74636800-74639200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr16:74636800-74639200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:74636800-74639400	Enhancers	Adipose Nuclei	Adipose
47	chr16:74637000-74639000	Weak transcription	Right Atrium	heart
48	chr16:74637400-74638200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr16:74637400-74638200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr16:74637400-74638600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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