Variant report

Variant	rs393329
Chromosome Location	chr16:12070422-12070423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:381)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:381 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr16:12070028-12070627	HL-60	blood:	n/a	n/a
2	JUND	chr16:12070317-12070620	HepG2	liver:	n/a	chr16:12070513-12070522
3	ELF1	chr16:12070275-12070769	K562	blood:	n/a	chr16:12070737-12070749
4	MXI1	chr16:12070323-12070581	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAZ	chr16:12069635-12072270	IMR90	lung:	n/a	chr16:12070760-12070770
6	POLR2A	chr16:12069916-12071737	Raji	blood:	n/a	n/a
7	POLR2A	chr16:12069402-12071168	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:12069631-12070837	K562	blood:	n/a	n/a
9	MAX	chr16:12070097-12070785	ECC-1	luminal epithelium:	n/a	chr16:12070760-12070770
10	TAF1	chr16:12070250-12070733	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZNF143	chr16:12070081-12070576	Hela-S3	cervix:	n/a	n/a
12	TBL1XR1	chr16:12070311-12070679	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr16:12070133-12070829	MCF-7	breast:	n/a	n/a
14	UBTF	chr16:12070168-12071715	K562	blood:	n/a	n/a
15	MAX	chr16:12070014-12070800	MCF-7	breast:	n/a	chr16:12070760-12070770
16	POLR2A	chr16:12069350-12071988	GM12878	blood:	n/a	n/a
17	TAF1	chr16:12070094-12070783	A549	lung:	n/a	n/a
18	SMARCB1	chr16:12069661-12071538	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr16:12070067-12070816	U87	brain:	n/a	n/a
20	POLR2A	chr16:12070278-12070784	A549	lung:	n/a	n/a
21	SP2	chr16:12070401-12070593	K562	blood:	n/a	n/a
22	TCF12	chr16:12070129-12070856	ECC-1	luminal epithelium:	n/a	n/a
23	E2F4	chr16:12070261-12070628	MCF10A-Er-Src	breast:	n/a	chr16:12070300-12070312 chr16:12070514-12070523 chr16:12070301-12070308 chr16:12070301-12070308 chr16:12070301-12070308
24	POLR2A	chr16:12069698-12071959	IMR90	lung:	n/a	n/a
25	MYBL2	chr16:12069890-12070643	HepG2	liver:	n/a	n/a
26	SIN3A	chr16:12070273-12070787	GM12878	blood:	n/a	n/a
27	SMC3	chr16:12070076-12070758	Hela-S3	cervix:	n/a	chr16:12070739-12070749
28	POLR2A	chr16:12069992-12070819	HCT-116	colon:	n/a	n/a
29	POLR2A	chr16:12070011-12070863	GM12891	blood:	n/a	n/a
30	POLR2A	chr16:12070134-12070912	GM12892	blood:	n/a	n/a
31	POLR2A	chr16:12070098-12070868	HL-60	blood:	n/a	n/a
32	EP300	chr16:12070202-12070579	HepG2	liver:	n/a	chr16:12070291-12070305
33	ELF1	chr16:12070209-12070679	HepG2	liver:	n/a	n/a
34	EGR1	chr16:12070080-12070558	K562	blood:	n/a	chr16:12070513-12070523
35	POLR2A	chr16:12070147-12070747	PANC-1	pancreas:	n/a	n/a
36	HCFC1	chr16:12070154-12070790	K562	blood:	n/a	n/a
37	POLR2A	chr16:12070064-12070934	H1-neurons	neurons:	n/a	n/a
38	TCF12	chr16:12070076-12070853	ECC-1	luminal epithelium:	n/a	n/a
39	FOXP2	chr16:12070303-12070625	SK-N-MC	brain:	n/a	n/a
40	MAX	chr16:12070088-12070738	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr16:12070200-12070886	U87	brain:	n/a	n/a
42	NFATC1	chr16:12070047-12070766	GM12878	blood:	n/a	n/a
43	POLR2A	chr16:12070134-12070865	HL-60	blood:	n/a	n/a
44	CTCF	chr16:12070320-12070470	WERI-Rb-1	eye:	n/a	n/a
45	ELF1	chr16:12070150-12070713	MCF-7	breast:	n/a	n/a
46	YY1	chr16:12070376-12070642	HCT-116	colon:	n/a	n/a
47	POLR2A	chr16:12069510-12071691	MCF10A-Er-Src	breast:	n/a	n/a
48	HEY1	chr16:12069646-12070819	K562	blood:	n/a	chr16:12070718-12070733 chr16:12070709-12070724
49	POLR2A	chr16:12070061-12070816	U87	brain:	n/a	n/a
50	REST	chr16:12070151-12070757	HepG2	liver:	n/a	chr16:12070389-12070398

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:12070416-12070466	AG09309	skin:	n/a
2	chr16:12070416-12070466	CMK	blood:	n/a
3	chr16:12070416-12070466	HAEpiC	amniotic membrane:	n/a
4	chr16:12070416-12070466	AG09319	gingival:	n/a
5	chr16:12070416-12070466	T-47D	breast:	n/a
6	chr16:12070416-12070466	SK-N-MC	brain:	n/a
7	chr16:12070416-12070466	HIPEpiC	eye:	n/a
8	chr16:12070416-12070466	HPAEpiC	pulmonary alveolar:	n/a
9	chr16:12070416-12070466	LNCaP	prostate:	n/a
10	chr16:12070416-12070466	HCPEpiC	choroid plexus:	n/a
11	chr16:12070416-12070466	HCF	heart:	n/a
12	chr16:12070416-12070466	AG10803	skin:	n/a
13	chr16:12070416-12070466	HRCEpiC	kidney:	n/a
14	chr16:12070416-12070466	MCF-7	breast:	n/a
15	chr16:12070416-12070466	HNPCEpiC	eye:	n/a
16	chr16:12070416-12070466	GM12891	blood:	n/a
17	chr16:12070416-12070466	U87	brain:	n/a
18	chr16:12070416-12070466	H1-hESC	embryonic stem cell:	embryo
19	chr16:12070416-12070466	SK-N-SH	brain:	n/a
20	chr16:12070416-12070466	NB4	blood:	n/a
21	chr16:12070416-12070466	MCF10A-Er-Src	breast:	n/a
22	chr16:12070416-12070466	SKMC	muscle:	n/a
23	chr16:12070416-12070466	ovcar-3	ovarian:	n/a
24	chr16:12070416-12070466	Caco-2	colon:	n/a
25	chr16:12070416-12070466	HUVEC	blood vessel:	n/a
26	chr16:12070416-12070466	NHBE	bronchial:	n/a
27	chr16:12070416-12070466	HRE	kidney:	n/a
28	chr16:12070416-12070466	GM12892	blood:	n/a
29	chr16:12070416-12070466	PANC-1	pancreas:	n/a
30	chr16:12070416-12070466	HL-60	blood:	n/a
31	chr16:12070416-12070466	BJ	skin:	n/a
32	chr16:12070416-12070466	SK-N-SH_RA	brain:	n/a
33	chr16:12070416-12070466	HCM	heart:	n/a
34	chr16:12070416-12070466	HEEpiC	esophagus:	n/a
35	chr16:12070416-12070466	NH-A	brain:	n/a
36	chr16:12070416-12070466	HCT-116	colon:	n/a
37	chr16:12070416-12070466	NHDF-neo	bronchial:	n/a
38	chr16:12070416-12070466	K562	blood:	n/a
39	chr16:12070416-12070466	HRPEpiC	eye:	n/a
40	chr16:12070416-12070466	HMEC	breast:	n/a
41	chr16:12070416-12070466	PFSK-1	brain:	n/a
42	chr16:12070416-12070466	BE2_C	brain:	n/a
43	chr16:12070416-12070466	GM19239	blood:	n/a
44	chr16:12070416-12070466	HepG2	liver:	n/a
45	chr16:12070416-12070466	HEK293	kidney:	embryo
46	chr16:12070416-12070466	NT2-D1	testis:	n/a
47	chr16:12070416-12070466	ProgFib	skin:	n/a
48	chr16:12070416-12070466	PrEC	prostate:	n/a
49	chr16:12070416-12070466	GM06990	blood:	n/a
50	chr16:12070416-12070466	IMR90	lung:	fetal

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:12006809..12011472-chr16:12069677..12072698,7	MCF-7	breast:
2	chr15:70389855..70390480-chr16:12070045..12070666,2	Hela-S3	cervix:
3	chr16:12070320..12071169-chr6:30711924..30712484,2	Hela-S3	cervix:
4	chr16:12069955..12070873-chr2:55277200..55277711,2	Hela-S3	cervix:
5	chr16:12070324..12072776-chr16:12897424..12899893,2	K562	blood:
6	chr16:12062509..12065114-chr16:12069207..12070961,2	MCF-7	breast:
7	chr16:12058363..12061770-chr16:12069205..12072370,4	MCF-7	breast:
8	chr16:12069629..12072468-chr16:12173207..12175470,2	MCF-7	breast:
9	chr16:12070393..12071024-chr19:10443895..10444545,2	NB4	blood:
10	chr16:12007711..12010113-chr16:12069770..12071913,2	MCF-7	breast:
11	chr16:12068975..12070484-chr16:12084406..12086978,2	K562	blood:
12	chr16:12068621..12072204-chr16:12129850..12134239,5	MCF-7	breast:
13	chr16:12070367..12070961-chrX:47092328..47093295,2	Hela-S3	cervix:
14	chr16:12006532..12011371-chr16:12068460..12073371,6	K562	blood:
15	chr1:234509055..234509726-chr16:12070259..12070961,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SNX29	TF binding region
SNX29	CpG island
ENSG00000115310	Chromatin interaction
ENSG00000241641	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000140332	Chromatin interaction
ENSG00000260224	Chromatin interaction
ENSG00000048462	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000231663	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000102226	Chromatin interaction
ENSG00000168275	Chromatin interaction
ENSG00000161847	Chromatin interaction
ENSG00000103381	Chromatin interaction
ENSG00000103342	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12922317	0.80[AMR][1000 genomes]
rs12930612	0.82[AMR][1000 genomes]
rs16958789	0.82[AMR][1000 genomes]
rs16958792	0.82[AMR][1000 genomes]
rs28473763	0.82[AMR][1000 genomes]
rs2869492	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3851005	0.84[AMR][1000 genomes]
rs8043644	0.82[AMR][1000 genomes]
rs8061496	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs393329	RP11-166B2.1	cis	Esophagus Muscularis	GTEx
rs393329	RP11-166B2.7	cis	Artery Tibial	GTEx
rs393329	RP11-166B2.1	cis	Artery Aorta	GTEx
rs393329	RP11-166B2.1	cis	Artery Tibial	GTEx
rs393329	RP11-166B2.7	cis	Adipose Subcutaneous	GTEx
rs393329	RP11-166B2.1	cis	Whole Blood	GTEx
rs393329	RP11-166B2.1	cis	Nerve Tibial	GTEx
rs393329	RP11-166B2.1	cis	Heart Left Ventricle	GTEx
rs393329	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs393329	RP11-166B2.1	cis	Thyroid	GTEx
rs393329	RP11-166B2.1	cis	Adipose Subcutaneous	GTEx
rs393329	RP11-166B2.1	cis	Stomach	GTEx
rs393329	RP11-166B2.1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12069400-12071200	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr16:12069400-12071200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr16:12069400-12071600	Active TSS	A549	lung
4	chr16:12069400-12072000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:12069400-12072200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr16:12069600-12071000	Active TSS	NHEK	skin
7	chr16:12069600-12071200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:12069600-12071200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr16:12069600-12071200	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr16:12069600-12071200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:12069600-12071200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:12069600-12071200	Active TSS	Esophagus	oesophagus
13	chr16:12069600-12071200	Active TSS	Fetal Intestine Large	intestine
14	chr16:12069600-12071200	Active TSS	HSMM	muscle
15	chr16:12069600-12071400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr16:12069600-12071400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr16:12069600-12071400	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr16:12069600-12071600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr16:12069600-12071600	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr16:12069600-12071800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr16:12069600-12071800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr16:12069600-12072000	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr16:12069600-12072600	Active TSS	Fetal Kidney	kidney
24	chr16:12069800-12071200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr16:12069800-12071400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr16:12069800-12071400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr16:12069800-12071400	Active TSS	Psoas Muscle	Psoas
28	chr16:12069800-12071600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:12069800-12071800	Active TSS	Right Atrium	heart
30	chr16:12069800-12072000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr16:12070000-12070800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr16:12070000-12071000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr16:12070000-12071000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr16:12070000-12071000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr16:12070000-12071000	Active TSS	Fetal Brain Male	brain
36	chr16:12070000-12071000	Active TSS	Fetal Thymus	thymus
37	chr16:12070000-12071000	Active TSS	Dnd41	blood
38	chr16:12070000-12071200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr16:12070000-12071200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr16:12070000-12071200	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr16:12070000-12071200	Active TSS	Brain Cingulate Gyrus	brain
42	chr16:12070000-12071200	Active TSS	Rectal Smooth Muscle	rectum
43	chr16:12070000-12071200	Active TSS	Small Intestine	intestine
44	chr16:12070000-12071200	Active TSS	Stomach Mucosa	stomach
45	chr16:12070000-12071200	Active TSS	Thymus	Thymus
46	chr16:12070000-12071200	Active TSS	HMEC	breast
47	chr16:12070000-12071200	Active TSS	K562	blood
48	chr16:12070000-12071400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:12070000-12071400	Active TSS	Brain Substantia Nigra	brain
50	chr16:12070000-12071400	Active TSS	Colon Smooth Muscle	Colon

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