Variant report

Variant	rs2287970
Chromosome Location	chr16:69599495-69599496
allele	C/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	POLR2A	chr16:69599284-69600825	HepG2	liver:	n/a	n/a
2	ZBTB7A	chr16:69599177-69601050	ECC-1	luminal epithelium:	n/a	n/a
3	SIN3A	chr16:69599420-69600103	GM12878	blood:	n/a	chr16:69599437-69599448 chr16:69599437-69599450
4	POLR2A	chr16:69599375-69601245	IMR90	lung:	n/a	n/a
5	MAX	chr16:69599347-69600083	SK-N-SH	brain:	n/a	chr16:69599673-69599683
6	ZNF384	chr16:69599041-69600202	K562	blood:	n/a	n/a
7	HDAC2	chr16:69599358-69600971	HepG2	liver:	n/a	n/a
8	CTCF	chr16:69599460-69599610	SAEC	small airway:	n/a	n/a
9	EGR1	chr16:69599200-69600588	HCT-116	colon:	n/a	chr16:69600444-69600458 chr16:69600469-69600483 chr16:69599651-69599661 chr16:69599882-69599896 chr16:69600445-69600455 chr16:69600442-69600457 chr16:69600443-69600456 chr16:69599836-69599845 chr16:69600443-69600456 chr16:69599782-69599792 chr16:69599856-69599866 chr16:69599854-69599863
10	POLR2A	chr16:69597676-69601656	GM12878	blood:	n/a	n/a
11	POLR2A	chr16:69599236-69600218	PANC-1	pancreas:	n/a	n/a
12	MAX	chr16:69599396-69600181	MCF-7	breast:	n/a	chr16:69599673-69599683
13	RAD21	chr16:69599354-69600022	SK-N-SH_RA	brain:	n/a	chr16:69599605-69599614 chr16:69599585-69599599 chr16:69599502-69599515 chr16:69599789-69599802
14	POLR2A	chr16:69599316-69600936	K562	blood:	n/a	n/a
15	POLR2A	chr16:69599369-69600690	HepG2	liver:	n/a	n/a
16	TEAD4	chr16:69599340-69600110	HepG2	liver:	n/a	n/a
17	RAD21	chr16:69599381-69599978	HepG2	liver:	n/a	chr16:69599605-69599614 chr16:69599585-69599599 chr16:69599502-69599515 chr16:69599789-69599802
18	POLR2A	chr16:69599388-69600169	K562	blood:	n/a	n/a
19	FOXA2	chr16:69599255-69599900	HepG2	liver:	n/a	n/a
20	TAF1	chr16:69599366-69600283	Hela-S3	cervix:	n/a	n/a
21	ZKSCAN1	chr16:69599427-69600114	Hela-S3	cervix:	n/a	n/a
22	E2F4	chr16:69599479-69599923	MCF10A-Er-Src	breast:	n/a	chr16:69599836-69599845 chr16:69599881-69599891 chr16:69599856-69599865 chr16:69599779-69599791 chr16:69599805-69599820
23	TAF1	chr16:69599438-69599651	GM12891	blood:	n/a	n/a
24	CTCF	chr16:69599480-69599630	WERI-Rb-1	eye:	n/a	chr16:69599603-69599616
25	MBD4	chr16:69599031-69600098	HepG2	liver:	n/a	n/a
26	MEF2A	chr16:69599441-69600050	GM12878	blood:	n/a	n/a
27	HEY1	chr16:69599156-69600273	HepG2	liver:	n/a	chr16:69600173-69600188 chr16:69599642-69599657 chr16:69599881-69599896
28	POLR2A	chr16:69599373-69600133	MCF10A-Er-Src	breast:	n/a	n/a
29	RELA	chr16:69599405-69600171	GM10847	blood:	n/a	n/a
30	RAD21	chr16:69599304-69600013	HepG2	liver:	n/a	chr16:69599605-69599614 chr16:69599585-69599599 chr16:69599502-69599515 chr16:69599789-69599802
31	RFX5	chr16:69599395-69600107	HepG2	liver:	n/a	n/a
32	SIN3AK20	chr16:69599352-69600478	HCT-116	colon:	n/a	n/a
33	EP300	chr16:69599442-69600233	ECC-1	luminal epithelium:	n/a	chr16:69600103-69600112 chr16:69599882-69599891 chr16:69599827-69599843 chr16:69599498-69599507
34	MAX	chr16:69599373-69600097	NB4	blood:	n/a	chr16:69599673-69599683
35	POLR2A	chr16:69599490-69599996	HepG2	liver:	n/a	n/a
36	CTCF	chr16:69599460-69599610	GM12869	blood:	n/a	n/a
37	CEBPB	chr16:69599460-69599680	HepG2	liver:	n/a	n/a
38	CTCF	chr16:69599480-69599630	HEEpiC	esophagus:	n/a	chr16:69599603-69599616
39	HCFC1	chr16:69599080-69602061	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr16:69599378-69600840	A549	lung:	n/a	n/a
41	POLR2A	chr16:69599331-69600493	H1-neurons	neurons:	n/a	n/a
42	YY1	chr16:69599394-69600529	ECC-1	luminal epithelium:	n/a	chr16:69600163-69600174 chr16:69599886-69599900 chr16:69599823-69599837 chr16:69599499-69599513 chr16:69600080-69600094 chr16:69600103-69600112 chr16:69599883-69599892 chr16:69599881-69599892 chr16:69599884-69599895 chr16:69600364-69600378 chr16:69599856-69599865
43	MAX	chr16:69599358-69601067	A549	lung:	n/a	chr16:69599673-69599683 chr16:69600596-69600606 chr16:69600301-69600310 chr16:69600446-69600456
44	POLR2A	chr16:69599368-69600420	HL-60	blood:	n/a	n/a
45	TEAD4	chr16:69599438-69600064	H1-hESC	embryonic stem cell:	n/a	n/a
46	YY1	chr16:69599418-69600101	H1-hESC	embryonic stem cell:	n/a	chr16:69599886-69599900 chr16:69599823-69599837 chr16:69599499-69599513 chr16:69600080-69600094 chr16:69599883-69599892 chr16:69599881-69599892 chr16:69599884-69599895 chr16:69599856-69599865
47	CCNT2	chr16:69599344-69600839	K562	blood:	n/a	chr16:69600471-69600480 chr16:69599856-69599865 chr16:69600293-69600302
48	POLR2A	chr16:69599329-69600324	HUVEC	blood vessel:	n/a	n/a
49	RCOR1	chr16:69599441-69600878	K562	blood:	n/a	n/a
50	CBX3	chr16:69599419-69600101	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:69372039..69374282-chr16:69599162..69601427,3	MCF-7	breast:
2	chr16:69599296..69599970-chr2:10260571..10261353,2	Hela-S3	cervix:
3	chr11:62608480..62609642-chr16:69599026..69599940,3	Hela-S3	cervix:
4	chr16:69457747..69460846-chr16:69598845..69601292,3	MCF-7	breast:
5	chr16:69457237..69459987-chr16:69598210..69601258,3	K562	blood:
6	chr16:69418494..69421401-chr16:69598786..69600485,2	K562	blood:
7	chr16:69372156..69375049-chr16:69597918..69599704,2	K562	blood:
8	chr16:69418062..69420388-chr16:69599340..69603002,4	K562	blood:
9	chr16:69598363..69600435-chr16:69788003..69790759,3	MCF-7	breast:
10	chr16:69598159..69601662-chr16:69788408..69790769,3	K562	blood:
11	chr16:69456628..69460851-chr16:69598482..69601931,4	MCF-7	breast:

Variant related genes	Relation type
NFAT5	TF binding region
ENSG00000132603	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000213380	Chromatin interaction
ENSG00000132604	Chromatin interaction
ENSG00000141101	Chromatin interaction
ENSG00000103018	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10852457	0.82[ASN][1000 genomes]
rs11075727	0.80[ASN][1000 genomes]
rs11642030	0.88[ASN][1000 genomes]
rs11642115	0.80[ASN][1000 genomes]
rs60099379	0.86[ASN][1000 genomes]
rs7190652	0.80[ASN][1000 genomes]
rs7196943	0.88[ASN][1000 genomes]
rs8045705	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1852	chr16:69566121-69610962	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases
2	esv3401540	chr16:69598976-69601824	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2287970	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69598000-69601600	Active TSS	Placenta Amnion	Placenta Amnion
2	chr16:69598000-69604600	Active TSS	GM12878-XiMat	blood
3	chr16:69598200-69602400	Active TSS	NHDF-Ad	bronchial
4	chr16:69598400-69599600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr16:69598400-69600800	Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr16:69598400-69601000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr16:69598400-69601200	Active TSS	Fetal Brain Female	brain
8	chr16:69598400-69601200	Active TSS	Stomach Smooth Muscle	stomach
9	chr16:69598400-69601800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr16:69598400-69601800	Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr16:69598400-69601800	Active TSS	Right Atrium	heart
12	chr16:69598400-69602000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr16:69598400-69602000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr16:69598400-69602400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr16:69598400-69602800	Active TSS	A549	lung
16	chr16:69598600-69600000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:69598600-69600800	Active TSS	Primary T cells fromperipheralblood	blood
18	chr16:69598600-69600800	Active TSS	Fetal Thymus	thymus
19	chr16:69598600-69601000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr16:69598600-69601000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr16:69598600-69601000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr16:69598600-69601000	Active TSS	Thymus	Thymus
23	chr16:69598600-69601200	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr16:69598600-69601400	Active TSS	Duodenum Mucosa	Duodenum
25	chr16:69598600-69601400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr16:69598600-69601400	Active TSS	Fetal Lung	lung
27	chr16:69598600-69601600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr16:69598600-69601600	Active TSS	HMEC	breast
29	chr16:69598600-69601800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:69598600-69601800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr16:69598600-69602200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr16:69598600-69602400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:69598600-69602400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr16:69598600-69602400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr16:69598600-69602400	Active TSS	K562	blood
36	chr16:69598600-69602600	Active TSS	HSMMtube	muscle
37	chr16:69598600-69603400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr16:69598800-69599600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr16:69598800-69600000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr16:69598800-69600800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:69598800-69601000	Active TSS	Brain Angular Gyrus	brain
42	chr16:69598800-69601000	Active TSS	Fetal Brain Male	brain
43	chr16:69598800-69601000	Active TSS	Fetal Muscle Leg	muscle
44	chr16:69598800-69601000	Active TSS	Psoas Muscle	Psoas
45	chr16:69598800-69601000	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr16:69598800-69601200	Active TSS	Brain Anterior Caudate	brain
47	chr16:69598800-69601200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr16:69598800-69601200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr16:69598800-69601400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr16:69598800-69601400	Active TSS	Fetal Intestine Large	intestine

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