Variant report

Variant	rs12105846
Chromosome Location	chr2:180128777-180128778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:
2	chr2:180127231..180129754-chr2:180137790..180140822,6	MCF-7	breast:
3	chr2:179315142..179317025-chr2:180127825..180130038,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237477	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000204311	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10164707	0.81[ASN][1000 genomes]
rs10170520	0.86[AFR][1000 genomes]
rs10177122	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10177402	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10181291	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10181464	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10182477	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10185803	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10194420	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10194534	1.00[EUR][1000 genomes]
rs10204985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10205999	0.87[AFR][1000 genomes]
rs10209183	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10209887	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10930858	0.86[AFR][1000 genomes]
rs10930859	0.97[EUR][1000 genomes]
rs11884516	0.85[AFR][1000 genomes]
rs11894870	0.83[AFR][1000 genomes]
rs11898291	0.84[AFR][1000 genomes]
rs12617002	0.96[ASN][1000 genomes]
rs12621023	0.92[EUR][1000 genomes]
rs12621115	0.87[ASN][1000 genomes]
rs12622075	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623243	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12693179	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12693181	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12693183	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12987285	0.81[ASN][1000 genomes]
rs13020645	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13026497	0.84[AFR][1000 genomes]
rs13382185	0.85[EUR][1000 genomes]
rs13384403	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13392996	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13396340	0.85[EUR][1000 genomes]
rs13414296	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13417919	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2007593	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28838656	0.85[EUR][1000 genomes]
rs57098667	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433770	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67043078	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6707081	0.87[AFR][1000 genomes]
rs6731614	0.96[ASN][1000 genomes]
rs6734121	0.87[AFR][1000 genomes]
rs6742739	0.83[AFR][1000 genomes]
rs6743412	0.84[ASN][1000 genomes]
rs6759983	0.93[ASN][1000 genomes]
rs7562730	0.84[AFR][1000 genomes]
rs7569887	0.84[ASN][1000 genomes]
rs7601366	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7608745	0.84[ASN][1000 genomes]
rs9288026	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3341099	chr2:180128207-180130605	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12105846	SESTD1	cis	multi-tissue	Pritchard
rs12105846	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180126400-180130200	Active TSS	Stomach Smooth Muscle	stomach
2	chr2:180127200-180129600	Active TSS	HMEC	breast
3	chr2:180127200-180129800	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr2:180127600-180128800	Flanking Active TSS	Dnd41	blood
5	chr2:180127600-180129600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:180127600-180129800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:180127600-180129800	Active TSS	Aorta	Aorta
8	chr2:180127600-180129800	Active TSS	Duodenum Mucosa	Duodenum
9	chr2:180127600-180130000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:180127800-180128800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr2:180127800-180128800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr2:180127800-180129000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:180127800-180129600	Active TSS	Fetal Stomach	stomach
14	chr2:180127800-180129800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr2:180127800-180129800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:180127800-180129800	Active TSS	Brain Angular Gyrus	brain
17	chr2:180127800-180129800	Active TSS	Brain Hippocampus Middle	brain
18	chr2:180127800-180129800	Active TSS	HSMMtube	muscle
19	chr2:180127800-180129800	Active TSS	NHLF	lung
20	chr2:180127800-180130000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:180127800-180130000	Active TSS	Fetal Kidney	kidney
22	chr2:180127800-180130000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr2:180127800-180130200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:180128000-180128800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr2:180128000-180128800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr2:180128000-180128800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:180128000-180128800	Active TSS	Fetal Brain Male	brain
28	chr2:180128000-180128800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr2:180128000-180129000	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
30	chr2:180128000-180129200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr2:180128000-180129600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:180128000-180129600	Active TSS	Primary B cells from peripheral blood	blood
33	chr2:180128000-180129600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:180128000-180129600	Active TSS	Brain Cingulate Gyrus	brain
35	chr2:180128000-180129800	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr2:180128000-180129800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:180128000-180130000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:180128000-180130000	Active TSS	Right Ventricle	heart
39	chr2:180128000-180130200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:180128200-180128800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr2:180128200-180128800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:180128200-180128800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
43	chr2:180128200-180128800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
44	chr2:180128200-180128800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:180128200-180128800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:180128200-180128800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:180128200-180128800	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
48	chr2:180128200-180128800	Flanking Active TSS	Placenta	Placenta
49	chr2:180128200-180128800	Flanking Active TSS	Fetal Thymus	thymus
50	chr2:180128200-180128800	Flanking Bivalent TSS/Enh	K562	blood

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