Variant report

Variant	rs2075158
Chromosome Location	chr16:11945231-11945232
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	MBD4	chr16:11944864-11946000	HepG2	liver:	n/a	n/a
2	SIN3AK20	chr16:11944586-11946428	MCF-7	breast:	n/a	n/a
3	BCL3	chr16:11944730-11945749	A549	lung:	n/a	chr16:11945166-11945175
4	SIN3AK20	chr16:11944879-11945801	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP2	chr16:11945171-11945719	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:11944974-11946133	MCF-7	breast:	n/a	n/a
7	TAF1	chr16:11944969-11945670	GM12891	blood:	n/a	n/a
8	POLR2A	chr16:11945003-11945734	GM12891	blood:	n/a	n/a
9	BCL3	chr16:11945151-11945766	A549	lung:	n/a	chr16:11945166-11945175
10	POLR2A	chr16:11944730-11946244	GM12892	blood:	n/a	n/a
11	WRNIP1	chr16:11944892-11945699	GM12878	blood:	n/a	n/a
12	POLR2A	chr16:11944995-11946035	PFSK-1	brain:	n/a	n/a
13	REST	chr16:11944820-11945985	HL-60	blood:	n/a	chr16:11945074-11945094 chr16:11944851-11944859
14	ELF1	chr16:11945189-11945799	K562	blood:	n/a	chr16:11945447-11945456 chr16:11945484-11945497 chr16:11945712-11945721 chr16:11945443-11945456
15	POLR2A	chr16:11945120-11945762	U87	brain:	n/a	n/a
16	TCF3	chr16:11945188-11945454	GM12878	blood:	n/a	n/a
17	UBTF	chr16:11944981-11946092	K562	blood:	n/a	n/a
18	NFIC	chr16:11945128-11945630	GM12878	blood:	n/a	n/a
19	POLR2A	chr16:11944979-11946108	GM12892	blood:	n/a	n/a
20	RUNX3	chr16:11944827-11946075	GM12878	blood:	n/a	n/a
21	YY1	chr16:11944954-11945597	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr16:11944962-11945921	GM18951	blood:	n/a	n/a
23	RFX5	chr16:11944969-11945750	HepG2	liver:	n/a	n/a
24	RELA	chr16:11944993-11945768	GM18951	blood:	n/a	n/a
25	MAZ	chr16:11944786-11946466	IMR90	lung:	n/a	chr16:11945727-11945736 chr16:11945935-11945945 chr16:11945456-11945466
26	TAF1	chr16:11944920-11945724	H1-neurons	neurons:	n/a	n/a
27	MYC	chr16:11944878-11945785	K562	blood:	n/a	chr16:11945727-11945736 chr16:11945456-11945466
28	USF1	chr16:11945217-11945612	SK-N-SH	brain:	n/a	n/a
29	HEY1	chr16:11944824-11946324	K562	blood:	n/a	n/a
30	POLR2A	chr16:11944921-11945932	U87	brain:	n/a	n/a
31	SPI1	chr16:11945070-11945838	GM12878	blood:	n/a	chr16:11945562-11945575
32	POLR2A	chr16:11945027-11945744	GM12892	blood:	n/a	n/a
33	NFIC	chr16:11944803-11945852	HepG2	liver:	n/a	n/a
34	MAX	chr16:11944820-11946317	MCF-7	breast:	n/a	chr16:11945727-11945736 chr16:11945935-11945945 chr16:11945456-11945466
35	SIN3AK20	chr16:11945048-11945951	A549	lung:	n/a	n/a
36	ETS1	chr16:11944907-11945812	K562	blood:	n/a	chr16:11945560-11945571 chr16:11945448-11945458
37	GABPA	chr16:11944791-11946415	MCF-7	breast:	n/a	chr16:11945420-11945434 chr16:11945423-11945432 chr16:11945565-11945572 chr16:11945423-11945434
38	ELK1	chr16:11945133-11945766	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr16:11944882-11945975	GM12892	blood:	n/a	n/a
40	E2F6	chr16:11944979-11946208	K562	blood:	n/a	chr16:11945424-11945433 chr16:11945709-11945718 chr16:11945458-11945470
41	MTA3	chr16:11944729-11946232	GM12878	blood:	n/a	n/a
42	TBL1XR1	chr16:11945156-11945727	K562	blood:	n/a	n/a
43	YY1	chr16:11944933-11945678	GM12891	blood:	n/a	n/a
44	ZNF263	chr16:11944900-11946340	HEK293-T-REx	kidney:	n/a	chr16:11945265-11945286
45	POLR2A	chr16:11944951-11945667	HepG2	liver:	n/a	n/a
46	GABPA	chr16:11945146-11945726	Hela-S3	cervix:	n/a	chr16:11945420-11945434 chr16:11945423-11945432 chr16:11945565-11945572 chr16:11945423-11945434
47	ATF3	chr16:11945076-11945668	A549	lung:	n/a	n/a
48	CHD2	chr16:11945199-11946324	HepG2	liver:	n/a	n/a
49	REST	chr16:11944945-11945632	SK-N-SH	brain:	n/a	chr16:11945074-11945094
50	MXI1	chr16:11944922-11946119	Hela-S3	cervix:	n/a	chr16:11945100-11945109 chr16:11945769-11945778

No.	Distal block	Cell Line	Cell type
1	chr16:11944315..11946480-chr16:12008232..12011350,3	K562	blood:
2	chr16:11891005..11893828-chr16:11944573..11948679,5	MCF-7	breast:
3	chr16:11944895..11945408-chrX:23801280..23802001,2	Hela-S3	cervix:
4	chr16:11889197..11895021-chr16:11943442..11946851,6	K562	blood:
5	chr16:11945202..11946733-chr16:11979732..11982221,2	MCF-7	breast:
6	chr16:11888083..11891789-chr16:11945035..11947357,4	MCF-7	breast:
7	chr1:27189467..27190290-chr16:11945079..11945643,2	HCT-116	colon:
8	chr16:11941713..11946689-chr16:12006948..12011249,6	MCF-7	breast:
9	chr16:11940299..11942446-chr16:11943353..11945680,3	K562	blood:
10	chr16:11936442..11940721-chr16:11941344..11946764,13	K562	blood:
11	chr16:11943912..11945965-chr16:12008319..12011491,4	MCF-7	breast:
12	chr12:27175449..27175969-chr16:11944994..11945891,2	HCT-116	colon:
13	chr16:11834777..11836567-chr16:11943909..11945629,3	K562	blood:
14	chr14:102227811..102228762-chr16:11944933..11945619,2	Hela-S3	cervix:
15	chr16:11874839..11876842-chr16:11943852..11946760,2	K562	blood:
16	chr16:11874200..11876842-chr16:11943852..11945564,2	K562	blood:

Variant related genes	Relation type
ENSG00000263307	TF binding region
RSL1D1	TF binding region
ENSG00000153066	Chromatin interaction
ENSG00000262420	Chromatin interaction
ENSG00000152944	Chromatin interaction
ENSG00000175793	Chromatin interaction
ENSG00000130066	Chromatin interaction
ENSG00000078304	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000122299	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000171490	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10852340	0.86[ASN][1000 genomes]
rs12924398	0.84[AMR][1000 genomes]
rs190461	0.82[EUR][1000 genomes]
rs2018199	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075159	0.81[EUR][1000 genomes]
rs2098722	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33619	0.88[CEU][hapmap]
rs33621	0.82[EUR][1000 genomes]
rs33623	0.88[CEU][hapmap]
rs33624	0.82[EUR][1000 genomes]
rs33629	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs33630	0.83[EUR][1000 genomes]
rs33631	0.88[CEU][hapmap]
rs33635	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs33648	0.90[EUR][1000 genomes]
rs33654	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs33655	0.88[CEU][hapmap]
rs33660	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs3743590	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs3971913	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40311	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs42424	0.88[EUR][1000 genomes]
rs4429311	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4493057	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4511557	0.88[CEU][hapmap]
rs4561483	0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs456325	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs6498250	0.87[ASN][1000 genomes]
rs7198817	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs7202234	0.88[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs8052900	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8061189	0.88[CEU][hapmap]
rs9927765	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][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	nsv482288	chr16:11776491-11946429	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2075158	TNFRSF17	cis	cerebellum	SCAN
rs2075158	GSPT1	Cis_1M	lymphoblastoid	RTeQTL
rs2075158	RSL1D1	cis	parietal	SCAN
rs2075158	TNFRSF17	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11943800-11946400	Active TSS	HMEC	breast
2	chr16:11943800-11946600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:11944000-11946200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr16:11944000-11946400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr16:11944000-11946400	Active TSS	Fetal Brain Female	brain
6	chr16:11944000-11946400	Active TSS	NHLF	lung
7	chr16:11944000-11946600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr16:11944000-11946600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr16:11944000-11946600	Active TSS	Psoas Muscle	Psoas
10	chr16:11944200-11945800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr16:11944200-11945800	Active TSS	Fetal Muscle Trunk	muscle
12	chr16:11944200-11945800	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr16:11944200-11946200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr16:11944200-11946200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr16:11944200-11946400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr16:11944200-11946400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr16:11944200-11946400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:11944200-11946400	Active TSS	Ovary	ovary
19	chr16:11944200-11946600	Active TSS	HSMM	muscle
20	chr16:11944200-11946800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr16:11944200-11946800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr16:11944200-11946800	Active TSS	GM12878-XiMat	blood
23	chr16:11944200-11947200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr16:11944400-11945600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr16:11944400-11945800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr16:11944400-11945800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr16:11944400-11946000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:11944400-11946000	Active TSS	Lung	lung
29	chr16:11944400-11946200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr16:11944400-11946200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:11944400-11946200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr16:11944400-11946200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr16:11944400-11946200	Active TSS	Aorta	Aorta
34	chr16:11944400-11946200	Active TSS	Fetal Intestine Large	intestine
35	chr16:11944400-11946200	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr16:11944400-11946400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:11944400-11946400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr16:11944400-11946400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr16:11944400-11946400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr16:11944400-11946400	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr16:11944400-11946400	Active TSS	Esophagus	oesophagus
42	chr16:11944400-11946400	Active TSS	Fetal Kidney	kidney
43	chr16:11944400-11946400	Bivalent/Poised TSS	HepG2	liver
44	chr16:11944400-11946400	Active TSS	HSMMtube	muscle
45	chr16:11944400-11946400	Active TSS	NHDF-Ad	bronchial
46	chr16:11944400-11946400	Active TSS	NHEK	skin
47	chr16:11944400-11946600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr16:11944400-11946600	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr16:11944400-11946600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr16:11944400-11946600	Active TSS	A549	lung

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