Variant report

Variant	rs10188759
Chromosome Location	chr2:179992766-179992767
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	chr2:179991457-179993112	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000238339	TF binding region
SESTD1	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10164707	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10164814	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10173710	0.81[EUR][1000 genomes]
rs10174774	0.86[TSI][hapmap]
rs10181291	0.83[EUR][1000 genomes]
rs10181464	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10196366	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10209887	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10439300	0.90[JPT][hapmap]
rs10803924	0.89[JPT][hapmap]
rs11898291	0.84[TSI][hapmap]
rs12617002	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs12621023	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs12621115	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12622075	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs12693179	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12987285	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12997314	0.84[TSI][hapmap]
rs13382185	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13396340	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13414296	0.84[EUR][1000 genomes]
rs13418701	0.84[TSI][hapmap]
rs1374378	0.84[TSI][hapmap]
rs1446674	0.82[TSI][hapmap]
rs17454311	0.95[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2289992	0.84[TSI][hapmap]
rs28838656	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs340320	0.86[JPT][hapmap]
rs340332	0.90[JPT][hapmap]
rs340334	0.90[JPT][hapmap]
rs4585064	0.82[TSI][hapmap]
rs6433760	0.84[TSI][hapmap]
rs6433764	0.84[TSI][hapmap]
rs6707081	0.84[TSI][hapmap]
rs6743405	0.84[TSI][hapmap]
rs6743412	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap]
rs6759983	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs7569887	0.84[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap]
rs7585600	0.84[TSI][hapmap]
rs7601366	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7608745	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs7608882	0.84[TSI][hapmap]
rs9288025	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs9288026	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][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	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	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
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10188759	SESTD1	cis	cerebellum	SCAN
rs10188759	SESTD1	cis	parietal	SCAN
rs10188759	SESTD1	cis	multi-tissue	Pritchard
rs10188759	SSFA2	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
2	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:179972600-180001800	Weak transcription	NHEK	skin
7	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
9	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
10	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
11	chr2:179973400-180012600	Weak transcription	NHLF	lung
12	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:179974400-179994200	Strong transcription	HepG2	liver
14	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:179976000-180004400	Weak transcription	Aorta	Aorta
16	chr2:179977400-180004400	Weak transcription	Lung	lung
17	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
18	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
19	chr2:179977600-180002000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:179978800-180004400	Weak transcription	Spleen	Spleen
22	chr2:179980000-180038800	Weak transcription	HMEC	breast
23	chr2:179980000-180056800	Weak transcription	HSMM	muscle
24	chr2:179980400-180005200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:179980400-180005600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:179981400-180001800	Weak transcription	Placenta	Placenta
27	chr2:179981400-180005000	Weak transcription	Ovary	ovary
28	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:179981600-179997600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:179981600-180004400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:179981600-180005000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:179981800-180005400	Weak transcription	Osteobl	bone
33	chr2:179982400-180004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:179982800-180004400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:179982800-180004600	Weak transcription	Fetal Brain Male	brain
36	chr2:179983600-180005000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:179984600-180003000	Weak transcription	Fetal Lung	lung
38	chr2:179984600-180004600	Weak transcription	HUVEC	blood vessel
39	chr2:179984800-180002000	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:179984800-180004200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:179984800-180005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
43	chr2:179985200-180004400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:179985200-180004400	Weak transcription	Fetal Stomach	stomach
45	chr2:179985400-180004000	Weak transcription	Dnd41	blood
46	chr2:179985600-179996200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:179985600-180005800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:179985800-180004000	Weak transcription	Fetal Intestine Large	intestine
49	chr2:179985800-180004400	Weak transcription	Fetal Brain Female	brain
50	chr2:179985800-180004400	Weak transcription	Left Ventricle	heart

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