Variant report

Variant	rs2016832
Chromosome Location	chr12:29471132-29471133
allele	A/C
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	CTCF	chr12:29470286-29471402	HCT-116	colon:	n/a	chr12:29470852-29470870
2	ZNF143	chr12:29470696-29471208	GM12878	blood:	n/a	n/a
3	RAD21	chr12:29470580-29471166	SK-N-SH_RA	brain:	n/a	chr12:29470850-29470869
4	RAD21	chr12:29470480-29471275	HCT-116	colon:	n/a	chr12:29470850-29470869
5	RAD21	chr12:29470648-29471138	MCF-7	breast:	n/a	chr12:29470850-29470869
6	SMC3	chr12:29470537-29471300	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr12:29470561-29471151	HepG2	liver:	n/a	chr12:29470852-29470870
8	CTCF	chr12:29470553-29471189	MCF-7	breast:	n/a	chr12:29470852-29470870
9	CTCF	chr12:29470592-29471195	K562	blood:	n/a	chr12:29470852-29470870
10	GATA3	chr12:29470560-29471291	SK-N-SH	brain:	n/a	chr12:29471266-29471276
11	CTCF	chr12:29470638-29471133	GM12878	blood:	n/a	chr12:29470852-29470870
12	RAD21	chr12:29470632-29471189	ECC-1	luminal epithelium:	n/a	chr12:29470850-29470869
13	CTCF	chr12:29470407-29471329	SK-N-SH	brain:	n/a	chr12:29470852-29470870
14	RAD21	chr12:29470343-29471398	SK-N-SH	brain:	n/a	chr12:29470850-29470869
15	MXI1	chr12:29470308-29471233	SK-N-SH	brain:	n/a	n/a
16	CTCF	chr12:29470662-29471137	ECC-1	luminal epithelium:	n/a	chr12:29470852-29470870
17	TFAP2A	chr12:29470768-29471201	Hela-S3	cervix:	n/a	chr12:29471002-29471016 chr12:29471002-29471017 chr12:29471004-29471014 chr12:29471002-29471016 chr12:29471002-29471016 chr12:29471004-29471014 chr12:29471002-29471016
18	CTCF	chr12:29470448-29471228	A549	lung:	n/a	chr12:29470852-29470870
19	REST	chr12:29470272-29471217	H1-neurons	neurons:	n/a	n/a
20	RAD21	chr12:29470634-29471136	A549	lung:	n/a	chr12:29470850-29470869
21	CTCF	chr12:29470586-29471172	T-47D	breast:	n/a	chr12:29470852-29470870
22	TFAP2C	chr12:29470728-29471200	Hela-S3	cervix:	n/a	chr12:29471000-29471015
23	RAD21	chr12:29470495-29471215	HCT-116	colon:	n/a	chr12:29470850-29470869
24	CTCF	chr12:29470595-29471197	A549	lung:	n/a	chr12:29470852-29470870
25	CTCF	chr12:29470687-29471159	MCF-7	breast:	n/a	chr12:29470852-29470870
26	CTCF	chr12:29470704-29471231	K562	blood:	n/a	chr12:29470852-29470870
27	CTCF	chr12:29470596-29471259	HCT-116	colon:	n/a	chr12:29470852-29470870
28	RAD21	chr12:29470528-29471140	MCF-7	breast:	n/a	chr12:29470850-29470869
29	RAD21	chr12:29470627-29471165	HepG2	liver:	n/a	chr12:29470850-29470869
30	RAD21	chr12:29470600-29471181	ECC-1	luminal epithelium:	n/a	chr12:29470850-29470869

Variant related genes	Relation type
FAR2	TF binding region
ENSG00000257176	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1006410	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1072724	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10743656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771517	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843376	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843385	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11050168	0.95[AFR][1000 genomes]
rs12301475	0.82[AFR][1000 genomes]
rs12578931	0.83[AMR][1000 genomes]
rs12581107	0.83[AMR][1000 genomes]
rs17715086	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2288128	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2288129	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2350315	0.80[EUR][1000 genomes]
rs3782505	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3782510	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4277150	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6487807	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299283	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7313552	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7315346	0.92[AFR][1000 genomes]
rs7358667	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7956305	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7961943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964831	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7980218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986072	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1795347	chr12:29458556-29471835	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2016832	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
3	chr12:29452800-29494200	Weak transcription	Lung	lung
4	chr12:29453000-29472800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:29453800-29480000	Weak transcription	Gastric	stomach
6	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
7	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
8	chr12:29459400-29471400	Weak transcription	Liver	Liver
9	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:29459600-29472800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:29459600-29476000	Weak transcription	Fetal Thymus	thymus
12	chr12:29460200-29476000	Weak transcription	Fetal Stomach	stomach
13	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
15	chr12:29463600-29474600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:29463800-29475400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:29464000-29476000	Weak transcription	Fetal Kidney	kidney
18	chr12:29464600-29474800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
20	chr12:29465800-29472800	Weak transcription	NHDF-Ad	bronchial
21	chr12:29466000-29474400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:29466000-29474600	Weak transcription	Placenta	Placenta
23	chr12:29466200-29472600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:29466200-29488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:29467200-29472800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:29467200-29473400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:29467200-29475800	Weak transcription	Pancreas	Pancrea
28	chr12:29467800-29474600	Weak transcription	Adipose Nuclei	Adipose
29	chr12:29468600-29471800	Weak transcription	Left Ventricle	heart
30	chr12:29468600-29491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:29469200-29471400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:29469400-29471200	Enhancers	Brain Substantia Nigra	brain
33	chr12:29469800-29471200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr12:29469800-29474800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:29470000-29471200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:29470000-29475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:29470000-29475200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:29470000-29475600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:29470000-29475800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:29470000-29486400	Weak transcription	Psoas Muscle	Psoas
41	chr12:29470000-29495600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:29470000-29500000	Weak transcription	K562	blood
43	chr12:29470200-29471200	Enhancers	HUVEC	blood vessel
44	chr12:29470200-29472800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:29470200-29472800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:29470200-29473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:29470200-29475000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:29470200-29475200	Weak transcription	Primary T cells from cord blood	blood
49	chr12:29470400-29474600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:29470400-29474800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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