Variant report

Variant	rs34959638
Chromosome Location	chr16:12070207-12070208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:233)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:233 , 50 per page) page: 1 2 3 4 5

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	ATF2	chr16:12070090-12070379	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr16:12069635-12072270	IMR90	lung:	n/a	chr16:12070760-12070770
4	POLR2A	chr16:12069916-12071737	Raji	blood:	n/a	n/a
5	POLR2A	chr16:12069402-12071168	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:12069631-12070837	K562	blood:	n/a	n/a
7	MAX	chr16:12070097-12070785	ECC-1	luminal epithelium:	n/a	chr16:12070760-12070770
8	ZNF143	chr16:12070081-12070576	Hela-S3	cervix:	n/a	n/a
9	SIN3AK20	chr16:12070133-12070829	MCF-7	breast:	n/a	n/a
10	UBTF	chr16:12070168-12071715	K562	blood:	n/a	n/a
11	MAX	chr16:12070014-12070800	MCF-7	breast:	n/a	chr16:12070760-12070770
12	POLR2A	chr16:12069350-12071988	GM12878	blood:	n/a	n/a
13	TAF1	chr16:12070094-12070783	A549	lung:	n/a	n/a
14	FOSL2	chr16:12069545-12070262	A549	lung:	n/a	n/a
15	SMARCB1	chr16:12069661-12071538	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr16:12070067-12070816	U87	brain:	n/a	n/a
17	TCF12	chr16:12070129-12070856	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr16:12069698-12071959	IMR90	lung:	n/a	n/a
19	MYBL2	chr16:12069890-12070643	HepG2	liver:	n/a	n/a
20	SMC3	chr16:12070076-12070758	Hela-S3	cervix:	n/a	chr16:12070739-12070749
21	POLR2A	chr16:12069992-12070819	HCT-116	colon:	n/a	n/a
22	POLR2A	chr16:12070011-12070863	GM12891	blood:	n/a	n/a
23	POLR2A	chr16:12070134-12070912	GM12892	blood:	n/a	n/a
24	POLR2A	chr16:12070098-12070868	HL-60	blood:	n/a	n/a
25	EP300	chr16:12070202-12070579	HepG2	liver:	n/a	chr16:12070291-12070305
26	EGR1	chr16:12070080-12070558	K562	blood:	n/a	chr16:12070513-12070523
27	POLR2A	chr16:12070147-12070747	PANC-1	pancreas:	n/a	n/a
28	NR2F2	chr16:12069539-12070406	K562	blood:	n/a	n/a
29	HCFC1	chr16:12070154-12070790	K562	blood:	n/a	n/a
30	POLR2A	chr16:12070064-12070934	H1-neurons	neurons:	n/a	n/a
31	TCF12	chr16:12070076-12070853	ECC-1	luminal epithelium:	n/a	n/a
32	MAX	chr16:12070088-12070738	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr16:12070200-12070886	U87	brain:	n/a	n/a
34	NFATC1	chr16:12070047-12070766	GM12878	blood:	n/a	n/a
35	POLR2A	chr16:12070134-12070865	HL-60	blood:	n/a	n/a
36	ELF1	chr16:12070150-12070713	MCF-7	breast:	n/a	n/a
37	POLR2A	chr16:12069510-12071691	MCF10A-Er-Src	breast:	n/a	n/a
38	HEY1	chr16:12069646-12070819	K562	blood:	n/a	chr16:12070718-12070733 chr16:12070709-12070724
39	POLR2A	chr16:12070061-12070816	U87	brain:	n/a	n/a
40	REST	chr16:12070151-12070757	HepG2	liver:	n/a	chr16:12070389-12070398
41	RCOR1	chr16:12069610-12071817	K562	blood:	n/a	n/a
42	SP1	chr16:12070143-12070748	A549	lung:	n/a	chr16:12070513-12070525 chr16:12070515-12070524 chr16:12070513-12070525
43	GTF3C2	chr16:12069473-12070432	Hela-S3	cervix:	n/a	n/a
44	EGR1	chr16:12070058-12070592	K562	blood:	n/a	chr16:12070513-12070523
45	IRF1	chr16:12070130-12070739	K562	blood:	n/a	chr16:12070287-12070307
46	TAF1	chr16:12070071-12070817	H1-hESC	embryonic stem cell:	n/a	n/a
47	GTF2F1	chr16:12069641-12070501	Hela-S3	cervix:	n/a	n/a
48	MXI1	chr16:12070087-12071077	HepG2	liver:	n/a	n/a
49	POLR2A	chr16:12069616-12071570	GM19193	blood:	n/a	n/a
50	TAF1	chr16:12070141-12070791	PFSK-1	brain:	n/a	n/a

No data

(count:11 , 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	chr16:12069955..12070873-chr2:55277200..55277711,2	Hela-S3	cervix:
4	chr16:12062509..12065114-chr16:12069207..12070961,2	MCF-7	breast:
5	chr16:12058363..12061770-chr16:12069205..12072370,4	MCF-7	breast:
6	chr16:12069629..12072468-chr16:12173207..12175470,2	MCF-7	breast:
7	chr16:12007711..12010113-chr16:12069770..12071913,2	MCF-7	breast:
8	chr16:12068975..12070484-chr16:12084406..12086978,2	K562	blood:
9	chr16:12068621..12072204-chr16:12129850..12134239,5	MCF-7	breast:
10	chr16:12006532..12011371-chr16:12068460..12073371,6	K562	blood:
11	chr12:57118643..57119257-chr16:12069612..12070224,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SNX29	TF binding region
ENSG00000196531	Chromatin interaction
ENSG00000241641	Chromatin interaction
ENSG00000140332	Chromatin interaction
ENSG00000260224	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000048462	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000048471	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11859104	0.90[EUR][1000 genomes]
rs12922317	0.91[EUR][1000 genomes]
rs12930612	0.91[EUR][1000 genomes]
rs16958789	0.91[EUR][1000 genomes]
rs16958792	0.91[EUR][1000 genomes]
rs28473763	0.95[EUR][1000 genomes]
rs3851005	0.89[EUR][1000 genomes]
rs67163308	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7206479	0.89[EUR][1000 genomes]
rs8043644	0.91[EUR][1000 genomes]
rs8061496	0.91[EUR][1000 genomes]

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	esv3414588	chr16:12068301-12070249	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34959638	RP11-166B2.1	cis	Esophagus Muscularis	GTEx
rs34959638	RP11-166B2.1	cis	Adipose Subcutaneous	GTEx
rs34959638	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs34959638	RP11-166B2.1	cis	Artery Tibial	GTEx
rs34959638	RP11-166B2.1	cis	Thyroid	GTEx
rs34959638	RP11-166B2.1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12069400-12070400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:12069400-12070400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr16:12069400-12070400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr16:12069400-12071200	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr16:12069400-12071200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr16:12069400-12071600	Active TSS	A549	lung
7	chr16:12069400-12072000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:12069400-12072200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr16:12069600-12070400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr16:12069600-12070400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr16:12069600-12070400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr16:12069600-12070400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr16:12069600-12070400	Flanking Active TSS	Colonic Mucosa	Colon
14	chr16:12069600-12070400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr16:12069600-12070400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr16:12069600-12070400	Flanking Active TSS	NH-A	brain
17	chr16:12069600-12071000	Active TSS	NHEK	skin
18	chr16:12069600-12071200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:12069600-12071200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr16:12069600-12071200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr16:12069600-12071200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:12069600-12071200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr16:12069600-12071200	Active TSS	Esophagus	oesophagus
24	chr16:12069600-12071200	Active TSS	Fetal Intestine Large	intestine
25	chr16:12069600-12071200	Active TSS	HSMM	muscle
26	chr16:12069600-12071400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr16:12069600-12071400	Active TSS	H1 Cell Line	embryonic stem cell
28	chr16:12069600-12071400	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr16:12069600-12071600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr16:12069600-12071600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr16:12069600-12071800	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr16:12069600-12071800	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr16:12069600-12072000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr16:12069600-12072600	Active TSS	Fetal Kidney	kidney
35	chr16:12069800-12070400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr16:12069800-12070400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr16:12069800-12070400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr16:12069800-12070400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr16:12069800-12070400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr16:12069800-12070400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr16:12069800-12070400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr16:12069800-12071200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr16:12069800-12071400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr16:12069800-12071400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr16:12069800-12071400	Active TSS	Psoas Muscle	Psoas
46	chr16:12069800-12071600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr16:12069800-12071800	Active TSS	Right Atrium	heart
48	chr16:12069800-12072000	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr16:12070000-12070800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr16:12070000-12071000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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