Variant report

Variant	rs12621023
Chromosome Location	chr2:180101777-180101778
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180099014..180101971-chr2:180103448..180105283,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10084229	0.89[JPT][hapmap]
rs10164707	0.90[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs10164814	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs10173710	0.83[ASN][1000 genomes]
rs10177122	0.92[EUR][1000 genomes]
rs10177402	0.92[EUR][1000 genomes]
rs10181291	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10181464	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10182477	0.92[EUR][1000 genomes]
rs10185803	0.92[EUR][1000 genomes]
rs10188759	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs10194420	0.92[EUR][1000 genomes]
rs10194534	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10196577	0.91[AFR][1000 genomes]
rs10204985	0.91[EUR][1000 genomes]
rs10208593	0.89[JPT][hapmap];0.89[YRI][hapmap]
rs10209183	0.91[EUR][1000 genomes]
rs10209887	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10930855	0.89[JPT][hapmap]
rs10930857	0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10930859	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1159257	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12105846	0.92[EUR][1000 genomes]
rs12621115	0.90[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12622075	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12693175	0.89[JPT][hapmap]
rs12693178	0.81[YRI][hapmap]
rs12693179	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12693181	0.84[EUR][1000 genomes]
rs12987285	0.90[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs13029576	0.88[JPT][hapmap]
rs13382185	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13384403	0.92[EUR][1000 genomes]
rs13389956	0.84[AFR][1000 genomes]
rs13396334	0.89[JPT][hapmap]
rs13396340	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13403102	0.85[ASN][1000 genomes]
rs13404037	0.89[JPT][hapmap]
rs13414296	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13420582	0.91[AFR][1000 genomes]
rs17363260	0.89[JPT][hapmap]
rs17454311	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs1968618	0.85[YRI][hapmap]
rs2007593	0.93[EUR][1000 genomes]
rs2289993	0.89[JPT][hapmap];0.92[YRI][hapmap]
rs2289994	0.89[JPT][hapmap];0.92[YRI][hapmap]
rs28838656	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4894081	0.81[YRI][hapmap]
rs57098667	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6433770	0.90[EUR][1000 genomes]
rs67043078	0.91[EUR][1000 genomes]
rs6743412	0.90[CEU][hapmap]
rs6759983	0.89[CEU][hapmap]
rs7569887	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs7601366	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7608745	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs9288025	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9288026	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12621023	SESTD1	cis	multi-tissue	Pritchard
rs12621023	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180067600-180104600	Weak transcription	Fetal Kidney	kidney
2	chr2:180068000-180103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:180083800-180102200	Weak transcription	HMEC	breast
4	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:180089800-180102000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:180090000-180102000	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:180090600-180102000	Weak transcription	Psoas Muscle	Psoas
8	chr2:180090600-180102400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:180091200-180102400	Weak transcription	Left Ventricle	heart
10	chr2:180091200-180104600	Weak transcription	Right Ventricle	heart
11	chr2:180091800-180101800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:180091800-180102000	Weak transcription	Fetal Brain Male	brain
13	chr2:180091800-180102200	Weak transcription	Fetal Brain Female	brain
14	chr2:180091800-180102200	Weak transcription	Fetal Heart	heart
15	chr2:180091800-180102400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
17	chr2:180092000-180102800	Weak transcription	Fetal Intestine Large	intestine
18	chr2:180092200-180101800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:180092200-180102400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:180092800-180102000	Weak transcription	Right Atrium	heart
21	chr2:180092800-180102000	Weak transcription	NHLF	lung
22	chr2:180092800-180104600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:180092800-180112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:180093000-180107800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:180094000-180102000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:180094200-180102000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:180095200-180104000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:180095400-180101800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:180096800-180102200	Weak transcription	HUVEC	blood vessel
30	chr2:180097000-180102800	Weak transcription	Fetal Intestine Small	intestine
31	chr2:180097200-180103600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:180098000-180103400	Enhancers	HepG2	liver
33	chr2:180098000-180105200	Weak transcription	Fetal Thymus	thymus
34	chr2:180098200-180102600	Weak transcription	Primary T cells from cord blood	blood
35	chr2:180098600-180102200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:180098600-180102400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
38	chr2:180098800-180101800	Weak transcription	A549	lung
39	chr2:180098800-180102400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:180099000-180103400	Weak transcription	Gastric	stomach
41	chr2:180099000-180103800	Weak transcription	Primary B cells from cord blood	blood
42	chr2:180099800-180102600	Weak transcription	GM12878-XiMat	blood
43	chr2:180100000-180103600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:180100400-180104000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:180100400-180104200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:180100600-180101800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:180100600-180102000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:180100600-180102000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:180100600-180103800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:180100600-180104000	Weak transcription	Primary B cells from peripheral blood	blood

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