Variant report

Variant	rs2341041
Chromosome Location	chr16:46853353-46853354
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	chr16:46852133..46853769-chr16:46855489..46857597,2	K562	blood:
2	chr16:46852902..46855463-chr16:46861590..46865288,6	K562	blood:

Variant related genes	Relation type
ENSG00000155330	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1009391	0.80[EUR][1000 genomes]
rs10468399	1.00[ASN][1000 genomes]
rs1641121	0.83[EUR][1000 genomes]
rs1641122	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1651654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166161	1.00[ASN][1000 genomes]
rs16948661	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189741	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17792604	1.00[ASN][1000 genomes]
rs183672	1.00[ASN][1000 genomes]
rs2341043	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs252721	1.00[ASN][1000 genomes]
rs252722	1.00[ASN][1000 genomes]
rs28174	1.00[ASN][1000 genomes]
rs28184	1.00[ASN][1000 genomes]
rs28485103	1.00[ASN][1000 genomes]
rs35444809	1.00[ASN][1000 genomes]
rs36310	1.00[ASN][1000 genomes]
rs36312	1.00[ASN][1000 genomes]
rs36462	1.00[ASN][1000 genomes]
rs36464	1.00[ASN][1000 genomes]
rs36471	1.00[ASN][1000 genomes]
rs36476	1.00[ASN][1000 genomes]
rs36481	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36483	1.00[ASN][1000 genomes]
rs40163	1.00[ASN][1000 genomes]
rs40355	1.00[ASN][1000 genomes]
rs41187	1.00[ASN][1000 genomes]
rs4141491	1.00[ASN][1000 genomes]
rs415018	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420865	1.00[ASN][1000 genomes]
rs42461	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4401068	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966606	1.00[ASN][1000 genomes]
rs4967393	1.00[ASN][1000 genomes]
rs4967576	0.80[EUR][1000 genomes]
rs57942848	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59064826	1.00[ASN][1000 genomes]
rs60500837	1.00[ASN][1000 genomes]
rs62057633	0.80[EUR][1000 genomes]
rs66508669	1.00[ASN][1000 genomes]
rs66804065	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67205347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67506574	1.00[ASN][1000 genomes]
rs67611436	1.00[ASN][1000 genomes]
rs67789219	1.00[ASN][1000 genomes]
rs68074363	1.00[ASN][1000 genomes]
rs68162608	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698418	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700582	1.00[ASN][1000 genomes]
rs712816	1.00[ASN][1000 genomes]
rs7186662	1.00[ASN][1000 genomes]
rs7187475	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190713	1.00[ASN][1000 genomes]
rs7197033	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198951	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7205668	1.00[ASN][1000 genomes]
rs72816835	1.00[ASN][1000 genomes]
rs72816877	1.00[ASN][1000 genomes]
rs794279	1.00[ASN][1000 genomes]
rs8044443	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8044684	1.00[ASN][1000 genomes]
rs8045353	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046748	1.00[ASN][1000 genomes]
rs8051017	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8058734	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs808432	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs808434	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808780	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808783	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799780	chr16:46386457-46875496	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv1059049	chr16:46721805-46859239	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv1067283	chr16:46801709-46885218	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	esv1797464	chr16:46820464-46857454	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2341041	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46824600-46856000	Weak transcription	Ovary	ovary
2	chr16:46824600-46863800	Weak transcription	Aorta	Aorta
3	chr16:46825000-46855200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr16:46829000-46855000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr16:46829000-46863400	Weak transcription	Fetal Stomach	stomach
6	chr16:46829600-46857600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr16:46829600-46860000	Weak transcription	Fetal Brain Male	brain
8	chr16:46831600-46854600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:46831600-46863000	Weak transcription	Fetal Muscle Leg	muscle
10	chr16:46831600-46863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr16:46832800-46856000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr16:46833600-46863000	Weak transcription	Fetal Thymus	thymus
13	chr16:46833600-46864200	Weak transcription	Pancreas	Pancrea
14	chr16:46834200-46863800	Weak transcription	Placenta	Placenta
15	chr16:46834600-46863800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr16:46834800-46854600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr16:46834800-46857600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr16:46835000-46855200	Weak transcription	Psoas Muscle	Psoas
19	chr16:46835000-46862800	Weak transcription	HSMMtube	muscle
20	chr16:46836800-46863000	Weak transcription	Colon Smooth Muscle	Colon
21	chr16:46837000-46854800	Weak transcription	Fetal Intestine Large	intestine
22	chr16:46837000-46857600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr16:46837000-46863000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr16:46839600-46855800	Weak transcription	Small Intestine	intestine
25	chr16:46840000-46856000	Weak transcription	HSMM	muscle
26	chr16:46840000-46857200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr16:46840200-46863800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr16:46841600-46863000	Weak transcription	Thymus	Thymus
29	chr16:46842000-46857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr16:46842400-46857600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr16:46844000-46854400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr16:46844000-46860600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr16:46844200-46856200	Weak transcription	NH-A	brain
34	chr16:46844200-46860200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:46844200-46862000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr16:46844200-46863200	Weak transcription	Adipose Nuclei	Adipose
37	chr16:46844400-46854600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr16:46844400-46856000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr16:46844400-46856200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr16:46844400-46860200	Weak transcription	Fetal Lung	lung
41	chr16:46844400-46860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr16:46844600-46860200	Weak transcription	HUVEC	blood vessel
43	chr16:46845000-46860000	Weak transcription	HepG2	liver
44	chr16:46845200-46863000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr16:46845200-46863400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr16:46847200-46854800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr16:46847400-46855000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr16:46848400-46864200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr16:46848600-46862400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr16:46849200-46855600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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