Variant report

Variant	rs1158872
Chromosome Location	chr2:180127703-180127704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:
2	chr2:180127231..180129754-chr2:180137790..180140822,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237477	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10170520	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10174774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10186198	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10192426	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10205390	0.83[JPT][hapmap]
rs10205999	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10439299	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10930858	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11894870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898291	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12997314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13026497	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383965	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13391602	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13418701	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1374378	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1446674	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs1907421	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2008989	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2008999	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2044479	0.92[YRI][hapmap]
rs2289992	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs2847	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4585064	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs6433757	0.80[EUR][1000 genomes]
rs6433760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433761	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433769	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734121	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736098	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6742739	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743405	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6756326	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562730	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7585600	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs7608882	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1158872	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
2	chr2:180118800-180128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:180119400-180128200	Weak transcription	Pancreas	Pancrea
4	chr2:180123800-180127800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:180123800-180127800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:180123800-180128000	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:180125400-180128000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:180125400-180128200	Weak transcription	Left Ventricle	heart
9	chr2:180125400-180128200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:180126200-180127800	Weak transcription	Stomach Mucosa	stomach
11	chr2:180126400-180128600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:180126400-180130200	Active TSS	Stomach Smooth Muscle	stomach
13	chr2:180126600-180127800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:180126600-180128200	Enhancers	Liver	Liver
15	chr2:180127000-180127800	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:180127000-180128000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr2:180127000-180128200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:180127000-180128200	Active TSS	HepG2	liver
19	chr2:180127200-180127800	Enhancers	Fetal Lung	lung
20	chr2:180127200-180128200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:180127200-180128200	Weak transcription	Small Intestine	intestine
22	chr2:180127200-180128400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr2:180127200-180129600	Active TSS	HMEC	breast
24	chr2:180127200-180129800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr2:180127400-180127800	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:180127400-180127800	Enhancers	Brain Angular Gyrus	brain
27	chr2:180127400-180127800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:180127400-180127800	Enhancers	Brain Substantia Nigra	brain
29	chr2:180127400-180127800	Flanking Active TSS	Fetal Brain Female	brain
30	chr2:180127400-180127800	Flanking Active TSS	Fetal Kidney	kidney
31	chr2:180127400-180127800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr2:180127400-180128000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:180127400-180128000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr2:180127400-180128000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:180127400-180128000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr2:180127400-180128400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr2:180127400-180128400	Flanking Active TSS	HUVEC	blood vessel
38	chr2:180127400-180128600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:180127400-180128600	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr2:180127400-180128600	Flanking Active TSS	Osteobl	bone
41	chr2:180127600-180127800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr2:180127600-180127800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr2:180127600-180127800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr2:180127600-180127800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:180127600-180127800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr2:180127600-180127800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:180127600-180127800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:180127600-180127800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:180127600-180127800	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr2:180127600-180127800	Flanking Active TSS	Fetal Stomach	stomach

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