Variant report

Variant	rs11649653
Chromosome Location	chr16:30918487-30918488
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30912499..30918732-chr16:30930262..30935475,13	MCF-7	breast:
2	chr16:30912902..30918884-chr16:30920570..30924921,9	MCF-7	breast:
3	chr16:30913031..30919294-chr16:30922948..30927916,8	MCF-7	breast:
4	chr16:30886579..30888306-chr16:30917088..30919338,2	MCF-7	breast:
5	chr16:30917528..30919524-chr16:30937722..30939647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230447	Chromatin interaction
ENSG00000099364	Chromatin interaction
ENSG00000265991	Chromatin interaction
ENSG00000260852	Chromatin interaction
ENSG00000260083	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1046276	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10782001	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10782002	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10871454	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs11076	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11150599	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs11150600	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11150601	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs11150604	0.94[GIH][hapmap];1.00[JPT][hapmap]
rs11640534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11640961	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap]
rs11862744	1.00[JPT][hapmap]
rs11864054	1.00[ASW][hapmap]
rs11864839	1.00[JPT][hapmap]
rs11865038	1.00[JPT][hapmap]
rs12445650	1.00[JPT][hapmap]
rs12599631	0.87[ASN][1000 genomes]
rs12917722	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12924903	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12926295	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs12928852	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12930545	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs12930657	0.87[ASN][1000 genomes]
rs12931046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs13336347	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13708	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1458201	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1458202	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1870293	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2032915	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs2054213	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2303222	1.00[JPT][hapmap]
rs2303223	1.00[JPT][hapmap]
rs2305880	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap]
rs2305884	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2359612	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs28360557	0.82[ASN][1000 genomes]
rs34873012	0.81[ASN][1000 genomes]
rs35468353	1.00[JPT][hapmap]
rs35675346	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs35733741	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751855	1.00[JPT][hapmap]
rs3813020	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs4468641	1.00[JPT][hapmap]
rs4889490	1.00[ASW][hapmap]
rs4889514	0.87[ASN][1000 genomes]
rs4889525	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4889571	0.87[ASN][1000 genomes]
rs4889599	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4889603	1.00[ASW][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4889604	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4889606	0.97[GIH][hapmap];0.89[JPT][hapmap]
rs4889609	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4889651	0.83[CHD][hapmap];0.88[JPT][hapmap]
rs4889653	0.83[CHD][hapmap];0.88[JPT][hapmap]
rs6565217	1.00[JPT][hapmap]
rs6950	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7184567	1.00[CHB][hapmap]
rs7185007	0.87[ASN][1000 genomes]
rs7196726	1.00[JPT][hapmap]
rs7197717	1.00[JPT][hapmap]
rs7199949	1.00[JPT][hapmap]
rs7200879	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7203999	0.89[JPT][hapmap]
rs7204459	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs7206511	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs72799341	0.82[ASN][1000 genomes]
rs7294	1.00[JPT][hapmap]
rs729482	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs732172	1.00[JPT][hapmap]
rs749670	1.00[JPT][hapmap]
rs749671	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs750952	1.00[JPT][hapmap]
rs8044030	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8046707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050588	0.82[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs8050894	1.00[JPT][hapmap]
rs8052245	1.00[ASN][1000 genomes]
rs8056842	1.00[JPT][hapmap]
rs8060857	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs8062719	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap]
rs8063565	0.88[JPT][hapmap]
rs881929	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs897986	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9319588	0.92[ASN][1000 genomes]
rs9923231	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs9926533	0.97[GIH][hapmap];0.89[JPT][hapmap]
rs9933843	1.00[CHD][hapmap];0.88[JPT][hapmap]
rs9934438	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs9938050	0.81[ASN][1000 genomes]
rs9938550	0.92[CHD][hapmap];0.82[ASN][1000 genomes]
rs9939417	0.81[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
5	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
6	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
7	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
8	nsv905733	chr16:30796919-31004812	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv869652	chr16:30799471-30951038	Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv833189	chr16:30819708-30960795	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	79 gene(s)	inside rSNPs	diseases
11	nsv833190	chr16:30845051-31007863	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
12	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
13	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
14	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
15	nsv905736	chr16:30900235-30995528	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
16	nsv905737	chr16:30900235-31014179	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
17	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
18	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
19	nsv905738	chr16:30906274-30973926	Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Triglycerides	20686565	GWAS catalog
Triglycerides	24097068	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11649653	ZNF668	cis	multi-tissue	Pritchard
rs11649653	BCKDK	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30913600-30932800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:30914000-30921400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr16:30914000-30933200	Weak transcription	Ovary	ovary
4	chr16:30914200-30919800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr16:30914400-30919000	Weak transcription	Colon Smooth Muscle	Colon
6	chr16:30914400-30920400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr16:30914600-30921400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:30914600-30921600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr16:30914600-30922400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr16:30914800-30919800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr16:30914800-30922000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr16:30914800-30931600	Weak transcription	Fetal Intestine Small	intestine
13	chr16:30914800-30932800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr16:30915200-30933000	Weak transcription	Right Atrium	heart
15	chr16:30915600-30921000	Weak transcription	Fetal Stomach	stomach
16	chr16:30915800-30918600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr16:30915800-30918800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr16:30915800-30918800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr16:30916000-30918600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr16:30916000-30918600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr16:30916000-30918600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr16:30916000-30918600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr16:30916000-30918600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr16:30916000-30918800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr16:30916000-30919200	Weak transcription	Thymus	Thymus
26	chr16:30916200-30919000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr16:30916200-30919000	Weak transcription	Fetal Muscle Leg	muscle
28	chr16:30916200-30919800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr16:30916200-30921400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr16:30916200-30921600	Weak transcription	Esophagus	oesophagus
31	chr16:30916200-30926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr16:30916400-30918600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr16:30916400-30918600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr16:30916400-30918800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr16:30916400-30919200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr16:30916600-30918800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr16:30917000-30918800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr16:30917000-30919200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr16:30917200-30918800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr16:30917400-30918600	Enhancers	HepG2	liver
41	chr16:30918200-30919000	Enhancers	Fetal Muscle Trunk	muscle
42	chr16:30918400-30919400	Enhancers	Primary T cells from cord blood	blood
43	chr16:30918400-30919400	Enhancers	Spleen	Spleen

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