Variant report

Variant	rs10164814
Chromosome Location	chr2:180059865-180059866
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	SPI1	chr2:180059857-180060216	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
SESTD1	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10164707	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[ASN][1000 genomes]
rs10173710	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10176829	0.87[ASN][1000 genomes]
rs10177122	0.80[ASN][1000 genomes]
rs10177402	0.80[ASN][1000 genomes]
rs10181291	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10181464	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10182477	0.80[ASN][1000 genomes]
rs10185803	0.80[ASN][1000 genomes]
rs10188759	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10194420	0.80[ASN][1000 genomes]
rs10196366	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204985	0.80[ASN][1000 genomes]
rs10209183	0.80[ASN][1000 genomes]
rs10209887	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs10439300	0.88[JPT][hapmap];0.84[YRI][hapmap]
rs10803924	0.86[JPT][hapmap]
rs1159257	0.80[CEU][hapmap]
rs12615736	0.85[EUR][1000 genomes]
rs12617002	0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs12621023	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs12621115	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[ASN][1000 genomes]
rs12622075	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs12623243	0.80[ASN][1000 genomes]
rs12693177	0.82[YRI][hapmap]
rs12693179	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12987285	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[ASN][1000 genomes]
rs13020645	0.80[ASN][1000 genomes]
rs13382185	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384403	0.80[ASN][1000 genomes]
rs13392996	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13396340	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13403102	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13414296	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13417919	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17454311	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1844763	0.87[YRI][hapmap]
rs2166534	0.93[YRI][hapmap]
rs28838656	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340320	0.86[JPT][hapmap]
rs340332	0.88[JPT][hapmap]
rs340334	0.88[JPT][hapmap]
rs4894082	0.89[YRI][hapmap]
rs57098667	0.80[ASN][1000 genomes]
rs67043078	0.80[ASN][1000 genomes]
rs6731614	0.80[ASN][1000 genomes]
rs6743412	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6759983	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs7420537	0.90[ASN][1000 genomes]
rs7569887	0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs7601366	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7608745	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs9288025	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs9288026	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs9653299	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10164814	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs10164814	SESTD1	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
2	chr2:180015000-180060600	Weak transcription	Lung	lung
3	chr2:180015400-180060600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:180032200-180067600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:180046400-180061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:180055200-180066800	Weak transcription	Fetal Kidney	kidney
7	chr2:180056200-180060400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:180056200-180066800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:180057200-180060000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:180058400-180060000	Enhancers	Adipose Nuclei	Adipose
11	chr2:180058800-180060200	Enhancers	HepG2	liver
12	chr2:180058800-180060400	Enhancers	Brain Hippocampus Middle	brain
13	chr2:180059000-180060000	Weak transcription	Primary B cells from cord blood	blood
14	chr2:180059000-180060000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:180059200-180060400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:180059400-180060400	Enhancers	Colon Smooth Muscle	Colon
17	chr2:180059600-180060000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:180059600-180060800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr2:180059600-180063400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:180059800-180060800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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