Variant report

Variant	rs2873480
Chromosome Location	chr16:81729108-81729109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172500840..172502745-chr16:81728547..81731083,2	MCF-7	breast:
2	chr16:81726984..81731246-chr16:81732450..81737036,4	MCF-7	breast:
3	chr16:81719217..81721536-chr16:81727180..81729899,2	MCF-7	breast:
4	chr16:81727343..81729891-chr16:81732559..81735043,3	K562	blood:
5	chr16:81729032..81729532-chr19:49995651..49996413,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLCG2-3	chr16:81729042-81731726	NONHSAT143954

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11150400	0.95[ASN][1000 genomes]
rs11641014	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11642818	0.86[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs11644560	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11646472	0.98[ASN][1000 genomes]
rs2317497	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751857	0.94[ASN][1000 genomes]
rs4281702	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4421970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4423411	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4888165	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888167	0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4889363	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4889364	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889365	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889366	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55669104	0.92[ASN][1000 genomes]
rs56303631	0.80[AMR][1000 genomes]
rs57869567	0.83[ASN][1000 genomes]
rs60107344	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67084911	0.81[ASN][1000 genomes]
rs68056614	0.98[ASN][1000 genomes]
rs74031237	0.97[ASN][1000 genomes]
rs74031241	0.97[ASN][1000 genomes]
rs753108	0.84[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
2	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	37 gene(s)	inside rSNPs	diseases
3	nsv907011	chr16:81639190-81757252	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active 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	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81688400-81736800	Weak transcription	NHDF-Ad	bronchial
2	chr16:81713200-81740600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr16:81713200-81744400	Weak transcription	Fetal Kidney	kidney
4	chr16:81721800-81748400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr16:81722000-81738400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr16:81724000-81743400	Strong transcription	HepG2	liver
7	chr16:81724400-81745800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr16:81724600-81733000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:81724600-81734000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr16:81724600-81743400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr16:81724600-81746000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr16:81724800-81732000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr16:81724800-81736400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr16:81724800-81740600	Strong transcription	Gastric	stomach
15	chr16:81724800-81741400	Strong transcription	Liver	Liver
16	chr16:81724800-81743200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr16:81724800-81743400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr16:81724800-81743400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr16:81724800-81743400	Strong transcription	Dnd41	blood
20	chr16:81724800-81744400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr16:81724800-81744600	Strong transcription	Primary T cells from cord blood	blood
22	chr16:81725000-81731600	Genic enhancers	Adipose Nuclei	Adipose
23	chr16:81725000-81733200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr16:81725000-81744400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr16:81725000-81744600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr16:81725000-81746000	Strong transcription	Thymus	Thymus
27	chr16:81725200-81729400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr16:81725200-81743200	Strong transcription	Primary B cells from cord blood	blood
29	chr16:81725400-81729600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr16:81725600-81729400	Enhancers	NH-A	brain
31	chr16:81725600-81739600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr16:81725600-81741200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr16:81725800-81729400	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr16:81725800-81729800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr16:81725800-81748200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr16:81726000-81729600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr16:81726000-81731000	Enhancers	Fetal Brain Female	brain
38	chr16:81726000-81732400	Genic enhancers	Fetal Muscle Leg	muscle
39	chr16:81726000-81732400	Genic enhancers	Fetal Stomach	stomach
40	chr16:81726000-81733800	Enhancers	Fetal Brain Male	brain
41	chr16:81726200-81729600	Genic enhancers	Brain Hippocampus Middle	brain
42	chr16:81726400-81730600	Genic enhancers	NHEK	skin
43	chr16:81726400-81732800	Genic enhancers	Fetal Lung	lung
44	chr16:81726600-81729600	Genic enhancers	Brain Anterior Caudate	brain
45	chr16:81726800-81729400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr16:81726800-81731400	Strong transcription	GM12878-XiMat	blood
47	chr16:81727000-81729200	Weak transcription	Right Atrium	heart
48	chr16:81727200-81731400	Genic enhancers	A549	lung
49	chr16:81727200-81740600	Weak transcription	Hela-S3	cervix
50	chr16:81727400-81730200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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