Variant report

Variant	rs342523
Chromosome Location	chr3:42587946-42587947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42586339..42588894-chr3:42591733..42594532,2	MCF-7	breast:
2	chr3:42587762..42590603-chr3:42632314..42633856,2	K562	blood:
3	chr3:42586177..42588807-chr3:42604036..42606237,3	K562	blood:
4	chr3:42576192..42579713-chr3:42587519..42590896,6	K562	blood:

Variant related genes	Relation type
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs13064311	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13066173	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13066333	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs168138	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs171057	0.93[ASN][1000 genomes]
rs2068278	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271181	0.92[ASN][1000 genomes]
rs2271184	0.94[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271187	0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2284305	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs237064	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2940407	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3095258	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs339656	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs339720	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs339721	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap]
rs339724	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs339729	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs339735	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs342524	0.95[ASN][1000 genomes]
rs342525	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs342526	0.97[ASN][1000 genomes]
rs342534	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342535	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs342538	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs383937	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3888651	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs398743	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs612362	0.94[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs637852	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs638904	0.80[ASN][1000 genomes]
rs651180	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs654761	0.85[EUR][1000 genomes]
rs663258	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs664813	0.88[EUR][1000 genomes]
rs665206	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6799021	0.91[ASN][1000 genomes]
rs704982	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs807863	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs82755	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs9311323	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311324	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9813479	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9819563	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9828279	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs342523	TMEM42	cis	cerebellum	SCAN
rs342523	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs342523	NKTR	cis	parietal	SCAN
rs342523	NKTR	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
2	chr3:42574800-42590200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:42575200-42589200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:42575600-42590000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:42577400-42590800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:42577400-42592800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:42577600-42592000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:42578400-42593200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:42578400-42593400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:42580000-42589800	Weak transcription	Primary T cells from cord blood	blood
13	chr3:42580800-42588600	Enhancers	Lung	lung
14	chr3:42581400-42589200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:42581800-42589000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:42581800-42589800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:42581800-42591200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:42581800-42594400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:42582000-42593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:42582000-42593600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:42582000-42594400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:42582200-42589800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:42582200-42594400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:42582800-42591600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:42582800-42592000	Weak transcription	Ovary	ovary
26	chr3:42583000-42590600	Weak transcription	Fetal Heart	heart
27	chr3:42583400-42589600	Weak transcription	Fetal Brain Female	brain
28	chr3:42584400-42589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:42584600-42590000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:42584800-42589600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:42585000-42590200	Enhancers	Liver	Liver
32	chr3:42585000-42590800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:42585200-42590400	Weak transcription	Esophagus	oesophagus
34	chr3:42585400-42588000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:42585600-42589200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:42586000-42591000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:42586000-42591200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:42586000-42593400	Weak transcription	NH-A	brain
39	chr3:42586200-42588200	Weak transcription	K562	blood
40	chr3:42586200-42588600	Weak transcription	Brain Anterior Caudate	brain
41	chr3:42586200-42588600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:42586200-42590000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:42586200-42595000	Weak transcription	Fetal Brain Male	brain
44	chr3:42586400-42588000	Weak transcription	GM12878-XiMat	blood
45	chr3:42586400-42591800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:42586400-42593200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:42586400-42593800	Weak transcription	Brain Angular Gyrus	brain
48	chr3:42586400-42594400	Weak transcription	NHEK	skin
49	chr3:42586600-42588400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:42586600-42588400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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