Variant report

Variant	rs13359
Chromosome Location	chr16:74482053-74482054
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	chr16:74481114..74483794-chr16:74490844..74493365,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLG1-1	chr16:74481325-74483790	ENSG00000260539.1

Variant related genes	Relation type
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1019572	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs1019573	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10500587	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11149722	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132843	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11639812	0.87[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11640632	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11643293	0.83[ASN][1000 genomes]
rs11644298	0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11647149	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11648868	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12325017	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs12445991	0.92[JPT][hapmap]
rs12446054	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12447531	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12448026	0.81[CEU][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs12598701	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13339161	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs1469140	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs1820262	0.92[CEU][hapmap]
rs2098754	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2288053	0.87[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303275	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2303278	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2303281	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs3785312	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3826239	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3851729	0.92[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs3851730	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4072450	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4438331	0.92[JPT][hapmap]
rs4600490	0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs4887772	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs4887776	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap]
rs4887777	0.88[CEU][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap]
rs4887779	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap]
rs4888238	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4888240	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4888242	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs4888253	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs4888256	0.81[CEU][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs4888262	0.92[JPT][hapmap]
rs6564117	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7185026	0.81[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7189123	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs7193583	0.88[CEU][hapmap]
rs7193959	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7194143	0.92[JPT][hapmap]
rs7203452	0.81[CEU][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs7204804	0.80[CHD][hapmap];0.92[JPT][hapmap]
rs7205258	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap]
rs7978	0.92[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs8045848	0.90[CHD][hapmap];0.84[JPT][hapmap]
rs8052923	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs8058133	0.92[JPT][hapmap]
rs8058692	0.81[CEU][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs8059869	0.81[CEU][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap]
rs918782	0.81[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs9888976	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs9923616	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9927073	0.92[JPT][hapmap]
rs9932831	0.92[JPT][hapmap]
rs9938833	0.80[CHD][hapmap];0.92[JPT][hapmap]

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	nsv1056566	chr16:74456589-74482388	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
15	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
16	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
17	nsv960308	chr16:74481305-74483524	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13359	RFWD3	cis	Skin Sun Exposed Lower leg	GTEx
rs13359	RFWD3	cis	Esophagus Mucosa	GTEx
rs13359	MLKL	cis	multi-tissue	Pritchard
rs13359	RFWD3	cis	multi-tissue	Pritchard
rs13359	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs13359	MLKL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74466600-74483200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr16:74467800-74483000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr16:74468200-74498400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:74468800-74483200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:74470400-74483000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr16:74470600-74483600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr16:74470600-74484800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr16:74471000-74485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr16:74471200-74483000	Weak transcription	Gastric	stomach
10	chr16:74471400-74482200	Weak transcription	Hela-S3	cervix
11	chr16:74471600-74483600	Weak transcription	GM12878-XiMat	blood
12	chr16:74472600-74485000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr16:74473000-74482200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr16:74473000-74483000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr16:74473000-74483200	Weak transcription	K562	blood
16	chr16:74473000-74484000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr16:74473000-74485400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr16:74473000-74486800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr16:74473000-74487000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr16:74473200-74483000	Weak transcription	Primary B cells from cord blood	blood
21	chr16:74473200-74483000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr16:74473200-74485600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr16:74473400-74483200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr16:74473600-74482200	Weak transcription	NHDF-Ad	bronchial
25	chr16:74473800-74483200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr16:74473800-74483200	Weak transcription	Dnd41	blood
27	chr16:74473800-74484000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr16:74474000-74485800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr16:74474800-74482600	Weak transcription	Ovary	ovary
30	chr16:74474800-74483400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr16:74475200-74482400	Weak transcription	NH-A	brain
32	chr16:74475400-74486800	Weak transcription	Fetal Kidney	kidney
33	chr16:74475600-74485000	Weak transcription	Aorta	Aorta
34	chr16:74476000-74482200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr16:74476000-74482800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr16:74476000-74483000	Weak transcription	HSMMtube	muscle
37	chr16:74476400-74482200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr16:74476400-74482800	Weak transcription	Liver	Liver
39	chr16:74476800-74483200	Weak transcription	Brain Anterior Caudate	brain
40	chr16:74479200-74484400	Enhancers	Adipose Nuclei	Adipose
41	chr16:74479800-74483200	Strong transcription	Fetal Stomach	stomach
42	chr16:74479800-74489400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr16:74480000-74486200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr16:74480000-74488200	Strong transcription	Primary T cells from cord blood	blood
45	chr16:74480200-74483200	Weak transcription	NHLF	lung
46	chr16:74480200-74483400	Weak transcription	Colon Smooth Muscle	Colon
47	chr16:74480400-74482200	Enhancers	Left Ventricle	heart
48	chr16:74480400-74482400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr16:74480400-74483400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr16:74480400-74484400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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