Variant report

Variant	rs8046445
Chromosome Location	chr16:30386262-30386263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30385968..30392864-chr16:30403786..30414800,30	MCF-7	breast:
2	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
3	chr16:30385721..30387689-chr16:30418863..30420571,2	MCF-7	breast:
4	chr16:30384243..30394929-chr16:30405602..30409736,14	K562	blood:
5	chr16:30378594..30387256-chr16:30387352..30391288,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179965	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000180209	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11150586	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs11642676	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11645581	0.88[EUR][1000 genomes]
rs11646130	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11862806	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11863150	0.83[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12446288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12447833	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12921440	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12930787	0.85[EUR][1000 genomes]
rs13333093	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35480350	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35598865	1.00[JPT][hapmap]
rs3574	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4465620	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4787642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4787643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4788409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4788413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4788414	0.80[EUR][1000 genomes]
rs62055459	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6565178	0.82[EUR][1000 genomes]
rs6565180	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6565182	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6565183	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68051857	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7203359	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73532600	0.89[EUR][1000 genomes]
rs8049108	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8050812	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8051096	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8060853	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9888967	0.86[ASN][1000 genomes]
rs9921711	0.85[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	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs8046445	LOC645287	trans	multi-tissue	Pritchard
rs8046445	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs8046445	SEPHS2	cis	cerebellum	SCAN
rs8046445	MAPK3	cis	parietal	SCAN
rs8046445	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs8046445	RP11-231C14.4	cis	Artery Tibial	GTEx
rs8046445	GDPD3	cis	cerebellum	SCAN
rs8046445	LOC23117	trans	multi-tissue	Pritchard
rs8046445	TBX6	cis	parietal	SCAN
rs8046445	SEPT1	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30381800-30388600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:30382800-30388000	Weak transcription	Colonic Mucosa	Colon
3	chr16:30382800-30388600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:30383000-30387000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:30383000-30387200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr16:30383000-30387400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr16:30383000-30387400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:30383000-30388000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr16:30383000-30388000	Weak transcription	Fetal Intestine Small	intestine
10	chr16:30383000-30388200	Weak transcription	Fetal Intestine Large	intestine
11	chr16:30383000-30388400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr16:30383000-30388400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:30383000-30388400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr16:30383000-30388400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr16:30383000-30388600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:30383000-30388600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr16:30383000-30388600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr16:30383000-30388600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr16:30383000-30388600	Weak transcription	Esophagus	oesophagus
20	chr16:30383000-30388600	Weak transcription	HUVEC	blood vessel
21	chr16:30383000-30388600	Weak transcription	NHEK	skin
22	chr16:30383000-30388600	Weak transcription	Osteobl	bone
23	chr16:30383200-30386800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr16:30383200-30386800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:30383200-30387000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr16:30383200-30387200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr16:30383200-30387200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr16:30383200-30387200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr16:30383200-30387600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr16:30383200-30387800	Weak transcription	Primary T cells from cord blood	blood
31	chr16:30383200-30387800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr16:30383200-30387800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr16:30383200-30387800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:30383200-30388000	Weak transcription	Primary B cells from cord blood	blood
35	chr16:30383200-30388000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr16:30383200-30388200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr16:30383200-30388400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr16:30383200-30388400	Weak transcription	Colon Smooth Muscle	Colon
39	chr16:30383200-30388400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr16:30383200-30388400	Weak transcription	Fetal Brain Male	brain
41	chr16:30383200-30388400	Weak transcription	Fetal Kidney	kidney
42	chr16:30383200-30388400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr16:30383200-30388400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr16:30383200-30388400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr16:30383200-30388600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr16:30383200-30388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr16:30383200-30388600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr16:30383200-30388600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr16:30383200-30388600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr16:30383200-30388600	Weak transcription	Adipose Nuclei	Adipose

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