Variant report

Variant	rs342525
Chromosome Location	chr3:42585461-42585462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42585374..42587081-chr3:42594734..42596739,2	K562	blood:
2	chr3:42584276..42586986-chr3:42587983..42591334,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs13064311	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs13066173	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs13066333	0.91[ASN][1000 genomes]
rs168138	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs171057	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2068278	0.83[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2271181	0.89[ASN][1000 genomes]
rs2271184	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2271187	0.94[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs2284305	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs237064	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2940407	0.94[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs3095258	0.88[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs339656	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs339720	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs339721	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs339724	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs339729	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs339735	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs342508	0.87[CEU][hapmap]
rs342523	0.83[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs342524	0.93[ASN][1000 genomes]
rs342526	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342534	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs342535	0.90[ASN][1000 genomes]
rs342538	0.92[ASN][1000 genomes]
rs383937	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3888651	0.86[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs398743	0.86[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs612362	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs637852	0.88[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs651180	0.82[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs663258	0.83[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6799021	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs82755	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs9311324	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs342525	NKTR	cis	cerebellum	SCAN
rs342525	NKTR	cis	parietal	SCAN
rs342525	NKTR	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
3	chr3:42562400-42586800	Weak transcription	Small Intestine	intestine
4	chr3:42571800-42586200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:42574800-42585600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:42574800-42590200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:42575200-42589200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:42575600-42590000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:42576600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:42577400-42590800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:42577400-42592800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:42577600-42592000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:42578400-42586400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:42578400-42586800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:42578400-42593200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:42578400-42593400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:42578600-42586200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:42580000-42589800	Weak transcription	Primary T cells from cord blood	blood
21	chr3:42580800-42588600	Enhancers	Lung	lung
22	chr3:42581000-42587000	Enhancers	Gastric	stomach
23	chr3:42581400-42589200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:42581800-42589000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:42581800-42589800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:42581800-42591200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:42581800-42594400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:42582000-42585800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:42582000-42593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:42582000-42593600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:42582000-42594400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:42582200-42586000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:42582200-42586400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:42582200-42587400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:42582200-42589800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:42582200-42594400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:42582800-42591600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:42582800-42592000	Weak transcription	Ovary	ovary
39	chr3:42583000-42585800	Weak transcription	Fetal Intestine Large	intestine
40	chr3:42583000-42585800	Weak transcription	Fetal Intestine Small	intestine
41	chr3:42583000-42586000	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:42583000-42590600	Weak transcription	Fetal Heart	heart
43	chr3:42583400-42589600	Weak transcription	Fetal Brain Female	brain
44	chr3:42584000-42587400	Enhancers	Pancreas	Pancrea
45	chr3:42584000-42587400	Enhancers	Stomach Mucosa	stomach
46	chr3:42584400-42589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:42584600-42587800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:42584600-42590000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:42584800-42586600	Enhancers	Right Ventricle	heart
50	chr3:42584800-42589600	Weak transcription	Monocytes-CD14+_RO01746	blood

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