Variant report

Variant	rs3774398
Chromosome Location	chr3:42595115-42595116
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	chr3:42592809..42595193-chr3:42597636..42599340,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2136012	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271181	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2271185	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271186	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2976533	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs339658	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs339725	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs339726	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs339727	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs339728	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs339733	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342507	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs342508	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs342521	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs342522	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342537	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4549	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs586082	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs587712	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs597498	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs607568	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs612733	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs614323	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs617722	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs627664	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs638836	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs639692	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs640689	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs663673	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs689251	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs704979	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8351	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs925457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9865109	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][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	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
2	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
rs3774398	NKTR	cis	Nerve Tibial	GTEx
rs3774398	NKTR	cis	parietal	SCAN
rs3774398	TMEM42	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:42587000-42602400	Weak transcription	Colonic Mucosa	Colon
3	chr3:42587400-42597000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:42587400-42597200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:42587400-42606800	Weak transcription	Small Intestine	intestine
6	chr3:42587800-42597000	Strong transcription	Fetal Thymus	thymus
7	chr3:42587800-42597000	Strong transcription	Thymus	Thymus
8	chr3:42587800-42611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:42588000-42613000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:42588400-42613000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:42589000-42611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:42589200-42611000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:42589400-42595400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:42589400-42596800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:42589400-42610800	Weak transcription	Stomach Mucosa	stomach
17	chr3:42589400-42611000	Strong transcription	Fetal Stomach	stomach
18	chr3:42589400-42612400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:42589400-42614000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:42589600-42611200	Strong transcription	Fetal Intestine Small	intestine
21	chr3:42589600-42611800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:42589800-42595800	Strong transcription	Primary T cells from cord blood	blood
23	chr3:42589800-42597000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:42589800-42597000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:42589800-42597200	Weak transcription	Hela-S3	cervix
26	chr3:42589800-42610600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:42589800-42611000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:42589800-42616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:42590000-42597000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:42590000-42597800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:42590000-42598600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:42590000-42603800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:42590000-42611600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr3:42590000-42612600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr3:42590200-42601600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:42590200-42611600	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:42590200-42611800	Strong transcription	Adipose Nuclei	Adipose
38	chr3:42590400-42597000	Strong transcription	Dnd41	blood
39	chr3:42590600-42597600	Strong transcription	GM12878-XiMat	blood
40	chr3:42590800-42599800	Strong transcription	HUVEC	blood vessel
41	chr3:42591000-42596000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr3:42591000-42605400	Strong transcription	Left Ventricle	heart
43	chr3:42591000-42609200	Strong transcription	Fetal Intestine Large	intestine
44	chr3:42591000-42614000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:42591200-42595800	Strong transcription	Brain Cingulate Gyrus	brain
46	chr3:42591200-42596800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:42591200-42597600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:42591200-42610400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:42591200-42611800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:42591400-42611200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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