Variant report

Variant	rs12994342
Chromosome Location	chr2:184009532-184009533
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:184008752..184011382-chr2:184012317..184013818,2	K562	blood:
2	chr2:184005599..184007720-chr2:184007957..184009877,2	K562	blood:
3	chr2:184007568..184011382-chr2:184012317..184014101,3	K562	blood:
4	chr2:183988409..183991229-chr2:184005605..184009543,5	MCF-7	breast:
5	chr2:184001895..184006122-chr2:184006438..184011885,6	K562	blood:
6	chr2:184006368..184007873-chr2:184008611..184010923,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163002	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11894093	0.98[ASN][1000 genomes]
rs11900745	0.86[AFR][1000 genomes]
rs11904060	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12105081	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12989618	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12992879	0.94[ASN][1000 genomes]
rs12993299	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13008910	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13023488	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13023969	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13024949	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13035624	0.88[CEU][hapmap]
rs1316974	0.81[ASN][1000 genomes]
rs1829121	0.86[ASN][1000 genomes]
rs2254866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2952363	0.90[CHB][hapmap]
rs34100542	0.90[ASN][1000 genomes]
rs34424877	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34426887	0.81[ASN][1000 genomes]
rs34591399	0.89[EUR][1000 genomes]
rs34743637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34767214	0.97[ASN][1000 genomes]
rs34921390	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34967913	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35290003	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35479161	0.87[ASN][1000 genomes]
rs35661877	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35672629	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35799804	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35873918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36021851	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36054361	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36100240	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3748884	0.93[ASN][1000 genomes]
rs3762477	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55865107	0.83[AFR][1000 genomes]
rs6434007	0.93[ASN][1000 genomes]
rs6434008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6434009	0.91[ASN][1000 genomes]
rs6705625	0.84[ASN][1000 genomes]
rs6705795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6709753	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715963	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6724387	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6729425	0.90[ASN][1000 genomes]
rs6730009	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6732406	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6740679	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6748218	0.90[ASN][1000 genomes]
rs6754901	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754938	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6758182	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6759975	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71427875	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs71427877	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71427878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71427880	0.83[ASN][1000 genomes]
rs73977848	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7571226	0.81[ASN][1000 genomes]
rs7587081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7592910	0.97[ASN][1000 genomes]
rs7597557	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9917390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv2763287	chr2:183939173-184037893	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12994342	SESTD1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183990000-184024400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:183990000-184050000	Weak transcription	Aorta	Aorta
3	chr2:183990200-184014200	Weak transcription	HSMMtube	muscle
4	chr2:183990200-184018800	Weak transcription	Placenta	Placenta
5	chr2:183990200-184036400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:183990600-184010200	Weak transcription	Brain Substantia Nigra	brain
7	chr2:183990600-184028600	Weak transcription	Colonic Mucosa	Colon
8	chr2:183990800-184025800	Weak transcription	Fetal Kidney	kidney
9	chr2:183990800-184031000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:183991000-184013400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:183991000-184018400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:183991000-184018400	Weak transcription	Gastric	stomach
13	chr2:183991000-184028600	Weak transcription	Right Ventricle	heart
14	chr2:183991000-184030400	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:183991000-184048400	Weak transcription	Brain Angular Gyrus	brain
16	chr2:183991000-184053400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:183991000-184055400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:183991200-184011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:183991200-184035400	Weak transcription	Fetal Brain Male	brain
20	chr2:183991400-184034000	Weak transcription	NHLF	lung
21	chr2:183991400-184049600	Weak transcription	NHDF-Ad	bronchial
22	chr2:183991600-184014200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:183991600-184029600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:183992400-184047600	Weak transcription	Hela-S3	cervix
25	chr2:183995200-184026000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:183996000-184013400	Weak transcription	Ovary	ovary
27	chr2:183996000-184026400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:183996400-184013600	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:183996400-184013800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:183996400-184018400	Weak transcription	Lung	lung
31	chr2:183996400-184025800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:184001000-184015000	Weak transcription	HSMM	muscle
33	chr2:184002200-184017600	Weak transcription	Pancreas	Pancrea
34	chr2:184004800-184011400	Weak transcription	Fetal Stomach	stomach
35	chr2:184005000-184025200	Weak transcription	Left Ventricle	heart
36	chr2:184005600-184010200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:184006400-184012000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:184006400-184013400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:184006600-184013000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:184006800-184009600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr2:184007600-184010200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr2:184007800-184016600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr2:184008000-184009600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
44	chr2:184008000-184009600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr2:184008000-184009600	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr2:184008000-184009600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
47	chr2:184008000-184012200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr2:184008000-184013600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:184008400-184011600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:184009000-184010200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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