Variant report

Variant	rs2078330
Chromosome Location	chr16:74580055-74580056
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: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11643608	0.81[JPT][hapmap]
rs2303279	0.81[JPT][hapmap]
rs3815826	0.81[JPT][hapmap]
rs3923202	0.91[EUR][1000 genomes]
rs3935784	0.81[JPT][hapmap]
rs4389167	0.91[EUR][1000 genomes]
rs4887778	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap]
rs4888272	1.00[CEU][hapmap]
rs8047350	1.00[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2078330	RFWD3	cis	Whole Blood	GTEx
rs2078330	RFWD3	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 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	chr16:74577200-74580200	Enhancers	HepG2	liver
16	chr16:74578400-74591200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr16:74578600-74582200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr16:74578600-74587600	Weak transcription	HUVEC	blood vessel
19	chr16:74578600-74589800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr16:74578600-74597400	Weak transcription	Pancreas	Pancrea
21	chr16:74579200-74597200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr16:74579400-74581000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr16:74579600-74580200	Enhancers	Liver	Liver
24	chr16:74579800-74580200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr16:74579800-74580200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr16:74579800-74580200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr16:74579800-74580200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr16:74579800-74580200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr16:74579800-74581000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr16:74580000-74580200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr16:74580000-74580200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr16:74580000-74580400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr16:74580000-74580600	Enhancers	Primary T helper cells fromperipheralblood	blood

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