Variant report

Variant	rs28838656
Chromosome Location	chr2:180060867-180060868
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	POLR2A	chr2:180060786-180060997	MCF-7	breast:	n/a	n/a
2	FOXA2	chr2:180060864-180061393	A549	lung:	n/a	n/a
3	POLR2A	chr2:180060713-180061373	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr2:180060865-180061100	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SESTD1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10164707	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10164814	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176829	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10177122	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10177402	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10181291	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10181464	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10182477	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10185803	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10188759	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10194420	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10194534	0.85[EUR][1000 genomes]
rs10196366	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10204985	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10209183	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10209887	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10439300	0.84[AFR][1000 genomes]
rs10930859	0.85[EUR][1000 genomes]
rs11687139	0.83[AFR][1000 genomes]
rs12105846	0.85[EUR][1000 genomes]
rs12617002	0.80[ASN][1000 genomes]
rs12621023	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12621115	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12622075	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12623243	0.80[ASN][1000 genomes]
rs12693179	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12987285	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13020645	0.80[ASN][1000 genomes]
rs13382185	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384403	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13392996	0.80[ASN][1000 genomes]
rs13396340	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13414296	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13417919	0.80[ASN][1000 genomes]
rs2007593	0.86[EUR][1000 genomes]
rs2166534	0.83[AFR][1000 genomes]
rs57098667	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6433770	0.83[EUR][1000 genomes]
rs67043078	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6731614	0.80[ASN][1000 genomes]
rs6743412	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6759983	0.80[ASN][1000 genomes]
rs7420537	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7569887	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7601366	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7608745	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9288026	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv1807721	chr2:180024167-180076733	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1826248	chr2:180056341-180072860	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv1842731	chr2:180056341-180076733	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv511167	chr2:180056341-180076733	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv3061	chr2:180057194-180095718	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv820056	chr2:180058961-180070761	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv14990	chr2:180060110-180083212	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv821830	chr2:180060110-180083212	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv2427556	chr2:180060320-180083338	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28838656	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180032200-180067600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:180046400-180061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:180055200-180066800	Weak transcription	Fetal Kidney	kidney
4	chr2:180056200-180066800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:180059600-180063400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:180060200-180066800	Weak transcription	HepG2	liver
7	chr2:180060400-180061200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:180060600-180061000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:180060600-180061000	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr2:180060600-180061000	Enhancers	Right Ventricle	heart
11	chr2:180060600-180061200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr2:180060600-180061200	Enhancers	Lung	lung

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