Variant report

Variant	rs2869492
Chromosome Location	chr16:12071341-12071342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr16:12069635-12072270	IMR90	lung:	n/a	chr16:12070760-12070770
2	POLR2A	chr16:12069916-12071737	Raji	blood:	n/a	n/a
3	UBTF	chr16:12070168-12071715	K562	blood:	n/a	n/a
4	POLR2A	chr16:12069350-12071988	GM12878	blood:	n/a	n/a
5	SMARCB1	chr16:12069661-12071538	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr16:12069698-12071959	IMR90	lung:	n/a	n/a
7	POLR2A	chr16:12069510-12071691	MCF10A-Er-Src	breast:	n/a	n/a
8	RCOR1	chr16:12069610-12071817	K562	blood:	n/a	n/a
9	BHLHE40	chr16:12071306-12071594	K562	blood:	n/a	n/a
10	RCOR1	chr16:12071319-12071528	K562	blood:	n/a	n/a
11	POLR2A	chr16:12069616-12071570	GM19193	blood:	n/a	n/a
12	POLR2A	chr16:12071160-12071628	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr16:12071225-12071969	U87	brain:	n/a	n/a
14	POLR2A	chr16:12071286-12071349	ProgFib	skin:	n/a	n/a
15	POLR2A	chr16:12071123-12071344	K562	blood:	n/a	n/a
16	POLR2A	chr16:12071340-12071653	Gliobla	brain:	n/a	n/a
17	POLR2A	chr16:12069784-12071528	GM18951	blood:	n/a	n/a
18	WRNIP1	chr16:12070864-12072578	GM12878	blood:	n/a	n/a
19	POLR2A	chr16:12071238-12071750	GM12878	blood:	n/a	n/a
20	POLR2A	chr16:12069964-12071572	GM12892	blood:	n/a	n/a
21	CHD2	chr16:12071040-12071553	Hela-S3	cervix:	n/a	n/a
22	MAZ	chr16:12071275-12071749	K562	blood:	n/a	n/a
23	POLR2A	chr16:12069293-12072542	GM12891	blood:	n/a	n/a
24	MTA3	chr16:12069599-12071500	GM12878	blood:	n/a	n/a
25	CHD1	chr16:12071137-12071807	GM12878	blood:	n/a	n/a
26	STAT5A	chr16:12069982-12071360	GM12878	blood:	n/a	n/a
27	REST	chr16:12069914-12071486	H1-neurons	neurons:	n/a	chr16:12070389-12070398
28	RCOR1	chr16:12071121-12071670	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr16:12069666-12071514	GM12892	blood:	n/a	n/a
30	POLR2A	chr16:12069746-12071941	MCF10A-Er-Src	breast:	n/a	n/a
31	MAFF	chr16:12071278-12071780	K562	blood:	n/a	n/a
32	MAZ	chr16:12069928-12071570	Hela-S3	cervix:	n/a	chr16:12070760-12070770
33	IKZF1	chr16:12071241-12071666	GM12878	blood:	n/a	n/a
34	GTF2F1	chr16:12071330-12071762	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr16:12069610-12071849	GM18505	blood:	n/a	n/a
36	MXI1	chr16:12069562-12072323	SK-N-SH	brain:	n/a	n/a
37	GATA2	chr16:12071185-12071570	SH-SY5Y	brain:	n/a	n/a
38	EBF1	chr16:12071000-12071384	GM12878	blood:	n/a	chr16:12071162-12071173 chr16:12071177-12071188

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:12006809..12011472-chr16:12069677..12072698,7	MCF-7	breast:
2	chr16:12070324..12072776-chr16:12897424..12899893,2	K562	blood:
3	chr16:12058363..12061770-chr16:12069205..12072370,4	MCF-7	breast:
4	chr16:12069629..12072468-chr16:12173207..12175470,2	MCF-7	breast:
5	chr16:12007711..12010113-chr16:12069770..12071913,2	MCF-7	breast:
6	chr16:12068621..12072204-chr16:12129850..12134239,5	MCF-7	breast:
7	chr16:12006532..12011371-chr16:12068460..12073371,6	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-166B2.1.1-1	chr16:12071293-12071707	ENSG00000260488.1

No data

Variant related genes	Relation type
ENSG00000234719	TF binding region
ENSG00000048471	Chromatin interaction
ENSG00000103381	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000241641	Chromatin interaction
ENSG00000048462	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11648404	0.92[CEU][hapmap]
rs11648938	0.92[CEU][hapmap]
rs11859104	0.82[AMR][1000 genomes]
rs12922317	0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs12930612	0.84[AMR][1000 genomes]
rs13332023	0.85[CHB][hapmap]
rs13339152	0.85[CHB][hapmap]
rs16958789	0.84[AMR][1000 genomes]
rs16958792	0.84[AMR][1000 genomes]
rs16958825	0.85[CHB][hapmap]
rs16958827	0.85[CHB][hapmap]
rs16958833	1.00[CHB][hapmap]
rs28473763	0.84[AMR][1000 genomes]
rs381584	0.85[CHB][hapmap]
rs3851005	0.92[MEX][hapmap];0.86[AMR][1000 genomes]
rs3862447	0.85[CHB][hapmap]
rs393329	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs442332	0.85[CHB][hapmap]
rs448737	1.00[CHB][hapmap]
rs7189138	0.85[CHB][hapmap]
rs7190848	0.85[CHB][hapmap]
rs7199459	1.00[CHB][hapmap]
rs7206479	0.82[AMR][1000 genomes]
rs8043644	0.84[AMR][1000 genomes]
rs8045634	0.88[CEU][hapmap]
rs8050827	0.88[CEU][hapmap]
rs8051349	0.92[CEU][hapmap]
rs8052559	0.85[CHB][hapmap]
rs8061496	0.84[AMR][1000 genomes]
rs8062691	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv962195	chr16:12053526-12071576	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv527197	chr16:12071341-12073800	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2869492	RP11-166B2.1	cis	Stomach	GTEx
rs2869492	RP11-166B2.1	cis	Nerve Tibial	GTEx
rs2869492	RP11-166B2.1	cis	Artery Tibial	GTEx
rs2869492	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2869492	RP11-166B2.1	cis	Esophagus Muscularis	GTEx
rs2869492	RP11-166B2.1	cis	Whole Blood	GTEx
rs2869492	RP11-166B2.1	cis	Thyroid	GTEx
rs2869492	GSPT1	cis	parietal	SCAN
rs2869492	RP11-166B2.1	cis	Artery Aorta	GTEx
rs2869492	RP11-166B2.1	cis	Heart Left Ventricle	GTEx
rs2869492	TNFRSF17	cis	cerebellum	SCAN
rs2869492	RP11-166B2.7	cis	Adipose Subcutaneous	GTEx
rs2869492	TNFRSF17	cis	parietal	SCAN
rs2869492	RP11-166B2.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12069400-12071600	Active TSS	A549	lung
2	chr16:12069400-12072000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr16:12069400-12072200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr16:12069600-12071400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr16:12069600-12071400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr16:12069600-12071400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr16:12069600-12071600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr16:12069600-12071600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr16:12069600-12071800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr16:12069600-12071800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr16:12069600-12072000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr16:12069600-12072600	Active TSS	Fetal Kidney	kidney
13	chr16:12069800-12071400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr16:12069800-12071400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr16:12069800-12071400	Active TSS	Psoas Muscle	Psoas
16	chr16:12069800-12071600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr16:12069800-12071800	Active TSS	Right Atrium	heart
18	chr16:12069800-12072000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr16:12070000-12071400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr16:12070000-12071400	Active TSS	Brain Substantia Nigra	brain
21	chr16:12070000-12071400	Active TSS	Colon Smooth Muscle	Colon
22	chr16:12070000-12071400	Active TSS	Gastric	stomach
23	chr16:12070000-12071400	Active TSS	Placenta Amnion	Placenta Amnion
24	chr16:12070000-12071400	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr16:12070000-12071400	Bivalent/Poised TSS	HepG2	liver
26	chr16:12070000-12071600	Active TSS	Aorta	Aorta
27	chr16:12070000-12071600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:12070000-12071600	Active TSS	Fetal Intestine Small	intestine
29	chr16:12070000-12071800	Active TSS	HSMMtube	muscle
30	chr16:12070000-12071800	Active TSS	NHDF-Ad	bronchial
31	chr16:12070000-12072000	Active TSS	Ovary	ovary
32	chr16:12070000-12072400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr16:12070200-12071400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr16:12070200-12071400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr16:12070200-12071400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr16:12070200-12071400	Active TSS	Fetal Stomach	stomach
37	chr16:12070200-12071400	Active TSS	Left Ventricle	heart
38	chr16:12070200-12071400	Active TSS	Lung	lung
39	chr16:12070200-12071400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr16:12070200-12071400	Active TSS	Osteobl	bone
41	chr16:12070200-12071800	Active TSS	NHLF	lung
42	chr16:12070200-12072000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr16:12070200-12072200	Active TSS	GM12878-XiMat	blood
44	chr16:12070200-12072400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr16:12070400-12072200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr16:12070800-12071400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr16:12070800-12071400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr16:12070800-12071600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr16:12070800-12071600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr16:12070800-12071600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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