Variant report

Variant	rs12693183
Chromosome Location	chr2:180129445-180129446
allele	G/T
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	MAX	chr2:180129099-180129997	HepG2	liver:	n/a	n/a
2	CEBPB	chr2:180128677-180130182	HepG2	liver:	n/a	chr2:180130075-180130088 chr2:180128847-180128858 chr2:180128845-180128856 chr2:180128845-180128858 chr2:180128847-180128856
3	POLR2A	chr2:180128542-180129740	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:180128316-180129842	H1-hESC	embryonic stem cell:	n/a	n/a
5	EGR1	chr2:180128909-180129517	K562	blood:	n/a	chr2:180129297-180129310 chr2:180129308-180129318 chr2:180129437-180129450 chr2:180128977-180128991 chr2:180129040-180129054 chr2:180129298-180129312 chr2:180129013-180129027 chr2:180129331-180129344
6	E2F6	chr2:180129342-180129881	A549	lung:	n/a	chr2:180129541-180129553 chr2:180129606-180129621 chr2:180129559-180129568
7	POLR2A	chr2:180128308-180129749	GM18526	blood:	n/a	n/a
8	MAX	chr2:180128083-180130069	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:180128558-180129802	Gliobla	brain:	n/a	n/a
10	HDAC2	chr2:180128145-180129955	HepG2	liver:	n/a	n/a
11	SIN3AK20	chr2:180128085-180129583	PANC-1	pancreas:	n/a	n/a
12	EP300	chr2:180129244-180130036	HepG2	liver:	n/a	chr2:180129245-180129254 chr2:180129591-180129607
13	CEBPD	chr2:180128885-180129849	HepG2	liver:	n/a	n/a
14	UBTF	chr2:180128410-180130025	K562	blood:	n/a	n/a
15	MAX	chr2:180128489-180129999	K562	blood:	n/a	n/a
16	MXI1	chr2:180127993-180129897	IMR90	lung:	n/a	n/a
17	TAF1	chr2:180129231-180129779	H1-neurons	neurons:	n/a	n/a
18	E2F6	chr2:180128362-180129972	K562	blood:	n/a	chr2:180129176-180129186 chr2:180129191-180129203 chr2:180129541-180129553 chr2:180129133-180129143 chr2:180129606-180129621 chr2:180129339-180129348 chr2:180129559-180129568
19	FOXA1	chr2:180129116-180129975	HepG2	liver:	n/a	n/a
20	TAF1	chr2:180129326-180129587	GM12878	blood:	n/a	n/a
21	ZBTB7A	chr2:180129322-180129954	ECC-1	luminal epithelium:	n/a	n/a
22	ZBTB7A	chr2:180129444-180129755	HepG2	liver:	n/a	n/a
23	CREB1	chr2:180129053-180129691	A549	lung:	n/a	n/a
24	HA-E2F1	chr2:180128225-180130113	MCF-7	breast:	n/a	chr2:180129176-180129186 chr2:180129191-180129203 chr2:180129541-180129553 chr2:180129133-180129143 chr2:180129606-180129621 chr2:180129339-180129348 chr2:180129559-180129568
25	BACH1	chr2:180129343-180129796	H1-hESC	embryonic stem cell:	n/a	n/a
26	YY1	chr2:180129094-180129593	GM12878	blood:	n/a	chr2:180129132-180129143 chr2:180129135-180129144 chr2:180129299-180129308 chr2:180129132-180129141 chr2:180129172-180129181 chr2:180129306-180129320 chr2:180129172-180129186 chr2:180129169-180129183 chr2:180129136-180129150
27	MXI1	chr2:180129168-180130078	HepG2	liver:	n/a	n/a
28	POLR2A	chr2:180128651-180129814	GM12892	blood:	n/a	n/a
29	PAX5	chr2:180128566-180129696	GM12892	blood:	n/a	chr2:180129552-180129571
30	MAX	chr2:180129233-180129928	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:180129033-180129748	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:180129095-180129756	HepG2	liver:	n/a	n/a
33	CHD2	chr2:180129185-180129727	Hela-S3	cervix:	n/a	chr2:180129565-180129575 chr2:180129570-180129580
34	MYBL2	chr2:180129222-180130057	HepG2	liver:	n/a	n/a
35	HEY1	chr2:180129349-180129522	K562	blood:	n/a	n/a
36	POLR2A	chr2:180129325-180129533	H1-hESC	embryonic stem cell:	n/a	n/a
37	CREB1	chr2:180129120-180129699	H1-hESC	embryonic stem cell:	n/a	n/a
38	SMARCB1	chr2:180128224-180129990	Hela-S3	cervix:	n/a	n/a
39	MAZ	chr2:180127821-180130020	IMR90	lung:	n/a	n/a
40	MAX	chr2:180129354-180130058	A549	lung:	n/a	n/a
41	POLR2A	chr2:180129316-180129610	H1-hESC	embryonic stem cell:	n/a	n/a
42	BHLHE40	chr2:180129188-180129549	GM12878	blood:	n/a	chr2:180129245-180129261
43	POLR2A	chr2:180129054-180129677	ECC-1	luminal epithelium:	n/a	n/a
44	MAX	chr2:180129069-180130029	MCF-7	breast:	n/a	n/a
45	POLR2A	chr2:180129178-180129806	HepG2	liver:	n/a	n/a
46	MAZ	chr2:180128240-180129896	Hela-S3	cervix:	n/a	n/a
47	FOXP2	chr2:180129126-180129739	PFSK-1	brain:	n/a	n/a
48	HA-E2F1	chr2:180128711-180129813	Hela-S3	cervix:	n/a	chr2:180129176-180129186 chr2:180129191-180129203 chr2:180129541-180129553 chr2:180129133-180129143 chr2:180129606-180129621 chr2:180129339-180129348 chr2:180129559-180129568
49	ZBTB7A	chr2:180129174-180129740	K562	blood:	n/a	n/a
50	POLR2A	chr2:180129065-180129644	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:
2	chr2:180127231..180129754-chr2:180137790..180140822,6	MCF-7	breast:
3	chr13:27745918..27746778-chr2:180129319..180129887,2	HCT-116	colon:
4	chr2:179315142..179317025-chr2:180127825..180130038,2	MCF-7	breast:

Variant related genes	Relation type
SESTD1	TF binding region
ENSG00000237477	Chromatin interaction
ENSG00000230641	Chromatin interaction
ENSG00000152484	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10164707	0.81[ASN][1000 genomes]
rs10177122	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177402	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10181291	0.84[ASN][1000 genomes]
rs10181464	0.81[ASN][1000 genomes]
rs10182477	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10185803	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10194420	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10194534	0.87[EUR][1000 genomes]
rs10204985	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10209183	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10209887	0.84[ASN][1000 genomes]
rs10930859	0.84[EUR][1000 genomes]
rs12105846	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12617002	0.89[ASN][1000 genomes]
rs12621115	0.84[ASN][1000 genomes]
rs12622075	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12623243	0.89[ASN][1000 genomes]
rs12693179	0.81[ASN][1000 genomes]
rs12693181	0.84[ASN][1000 genomes]
rs12987285	0.81[ASN][1000 genomes]
rs13020645	0.89[ASN][1000 genomes]
rs13384403	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13392996	0.89[ASN][1000 genomes]
rs13414296	0.81[ASN][1000 genomes]
rs13417919	0.89[ASN][1000 genomes]
rs2007593	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57098667	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6433770	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67043078	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6731614	0.89[ASN][1000 genomes]
rs6743412	0.81[ASN][1000 genomes]
rs6759983	0.86[ASN][1000 genomes]
rs7569887	0.81[ASN][1000 genomes]
rs7601366	0.81[ASN][1000 genomes]
rs7608745	0.81[ASN][1000 genomes]
rs9288026	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3341099	chr2:180128207-180130605	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12693183	SESTD1	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180126400-180130200	Active TSS	Stomach Smooth Muscle	stomach
2	chr2:180127200-180129600	Active TSS	HMEC	breast
3	chr2:180127200-180129800	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr2:180127600-180129600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:180127600-180129800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:180127600-180129800	Active TSS	Aorta	Aorta
7	chr2:180127600-180129800	Active TSS	Duodenum Mucosa	Duodenum
8	chr2:180127600-180130000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:180127800-180129600	Active TSS	Fetal Stomach	stomach
10	chr2:180127800-180129800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:180127800-180129800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:180127800-180129800	Active TSS	Brain Angular Gyrus	brain
13	chr2:180127800-180129800	Active TSS	Brain Hippocampus Middle	brain
14	chr2:180127800-180129800	Active TSS	HSMMtube	muscle
15	chr2:180127800-180129800	Active TSS	NHLF	lung
16	chr2:180127800-180130000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:180127800-180130000	Active TSS	Fetal Kidney	kidney
18	chr2:180127800-180130000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:180127800-180130200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:180128000-180129600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:180128000-180129600	Active TSS	Primary B cells from peripheral blood	blood
22	chr2:180128000-180129600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:180128000-180129600	Active TSS	Brain Cingulate Gyrus	brain
24	chr2:180128000-180129800	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr2:180128000-180129800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:180128000-180130000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:180128000-180130000	Active TSS	Right Ventricle	heart
28	chr2:180128000-180130200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:180128200-180129600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:180128200-180129600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:180128200-180129600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:180128200-180129600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:180128200-180129600	Active TSS	Esophagus	oesophagus
34	chr2:180128200-180129600	Active TSS	Fetal Muscle Trunk	muscle
35	chr2:180128200-180129600	Active TSS	Lung	lung
36	chr2:180128200-180129600	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr2:180128200-180129600	Active TSS	Small Intestine	intestine
38	chr2:180128200-180129600	Active TSS	Thymus	Thymus
39	chr2:180128200-180129600	Active TSS	GM12878-XiMat	blood
40	chr2:180128200-180129600	Active TSS	NHEK	skin
41	chr2:180128200-180129800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:180128200-180129800	Active TSS	Brain Anterior Caudate	brain
43	chr2:180128200-180129800	Active TSS	Brain Substantia Nigra	brain
44	chr2:180128200-180129800	Active TSS	Colon Smooth Muscle	Colon
45	chr2:180128200-180129800	Active TSS	Gastric	stomach
46	chr2:180128200-180129800	Active TSS	Spleen	Spleen
47	chr2:180128200-180129800	Active TSS	HSMM	muscle
48	chr2:180128200-180129800	Active TSS	NHDF-Ad	bronchial
49	chr2:180128200-180130000	Active TSS	H9 Cell Line	embryonic stem cell
50	chr2:180128200-180130000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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