Variant report

Variant	rs62037727
Chromosome Location	chr16:12130572-12130573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF3	chr16:12130514-12130672	GM12878	blood:	n/a	chr16:12130600-12130609 chr16:12130597-12130612
2	TCF12	chr16:12130466-12130705	GM12878	blood:	n/a	n/a
3	PBX3	chr16:12130492-12130640	GM12878	blood:	n/a	n/a
4	CEBPB	chr16:12130470-12130681	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:12073934..12076136-chr16:12129849..12132030,2	K562	blood:
2	chr16:12118157..12118838-chr16:12130477..12131347,2	MCF-7	breast:
3	chr16:12070167..12072046-chr16:12129596..12132350,2	K562	blood:
4	chr16:12068621..12072204-chr16:12129850..12134239,5	MCF-7	breast:

Variant related genes	Relation type
SNX29	TF binding region
ENSG00000234719	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000260488	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11075042	1.00[ASN][1000 genomes]
rs11859105	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11859378	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11859602	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11859670	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11859801	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11862031	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11863344	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11863772	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11864775	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11865036	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11865132	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11865547	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2257492	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2865105	1.00[ASN][1000 genomes]
rs34321532	0.93[ASN][1000 genomes]
rs34701893	0.93[ASN][1000 genomes]
rs35106911	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826097	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3826098	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851006	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851007	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3862465	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs459292	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55719789	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55788618	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55845335	0.89[ASN][1000 genomes]
rs55933754	0.86[ASN][1000 genomes]
rs55995758	0.93[ASN][1000 genomes]
rs56166842	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56325311	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56363861	0.85[ASN][1000 genomes]
rs62037728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037734	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62037735	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62037736	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037739	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037740	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037741	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7184186	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7186759	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7192463	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7196418	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7200173	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7202235	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7202328	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7202330	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7202375	0.96[ASN][1000 genomes]
rs72784623	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72784632	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8044821	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8045202	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8051298	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052866	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8057116	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv977110	chr16:12123355-12146787	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62037727	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12098400-12136000	Weak transcription	Fetal Stomach	stomach
4	chr16:12099600-12135200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr16:12105200-12142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:12109800-12142200	Weak transcription	Gastric	stomach
8	chr16:12112000-12142200	Weak transcription	NHLF	lung
9	chr16:12112000-12144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr16:12115200-12140600	Weak transcription	Thymus	Thymus
11	chr16:12116200-12141000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr16:12116800-12130800	Weak transcription	Fetal Kidney	kidney
13	chr16:12117200-12140400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr16:12118200-12140400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:12118400-12130800	Weak transcription	Right Ventricle	heart
17	chr16:12118600-12130800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr16:12118600-12130800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr16:12119200-12146400	Weak transcription	Fetal Lung	lung
20	chr16:12119400-12142000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr16:12119600-12130800	Weak transcription	Pancreas	Pancrea
22	chr16:12119600-12148400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr16:12119800-12130800	Weak transcription	HepG2	liver
24	chr16:12120200-12132600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr16:12121000-12142200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr16:12121200-12130800	Weak transcription	Fetal Muscle Leg	muscle
27	chr16:12121200-12130800	Weak transcription	Spleen	Spleen
28	chr16:12121200-12132600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr16:12121400-12130600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr16:12121400-12155000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr16:12121600-12140200	Weak transcription	Fetal Thymus	thymus
32	chr16:12121600-12142000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr16:12121800-12140000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr16:12122200-12132600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr16:12122200-12140200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr16:12122200-12140800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr16:12122800-12144000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr16:12124400-12156600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr16:12124800-12130800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr16:12124800-12136600	Weak transcription	Primary T cells from cord blood	blood
41	chr16:12124800-12142000	Weak transcription	Esophagus	oesophagus
42	chr16:12124800-12155000	Weak transcription	NH-A	brain
43	chr16:12125000-12140200	Weak transcription	Lung	lung
44	chr16:12125200-12130600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr16:12125200-12136800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:12125800-12131600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr16:12126400-12150000	Weak transcription	Small Intestine	intestine
48	chr16:12126600-12131200	Enhancers	Primary B cells from cord blood	blood
49	chr16:12127400-12131000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr16:12127400-12131800	Enhancers	Primary B cells from peripheral blood	blood

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