Variant report

Variant	rs3861690
Chromosome Location	chr1:85464509-85464510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:85459671-85465061	GM12892	blood:	n/a	n/a
2	TCF7L2	chr1:85463483-85464827	PANC-1	pancreas:	n/a	n/a
3	EBF1	chr1:85464485-85464813	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:85461494-85464994	GM12892	blood:	n/a	n/a
5	ZNF143	chr1:85464457-85464793	GM12878	blood:	n/a	n/a
6	MTA3	chr1:85464165-85465112	GM12878	blood:	n/a	n/a
7	WRNIP1	chr1:85464037-85465106	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:85459795-85464999	GM12878	blood:	n/a	n/a
9	RCOR1	chr1:85464116-85464636	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:85460981-85465011	GM19099	blood:	n/a	n/a
11	POLR2A	chr1:85464372-85464883	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:85461099-85464971	GM19193	blood:	n/a	n/a
13	SUZ12	chr1:85461677-85465137	NT2-D1	testis:	n/a	n/a
14	POLR2A	chr1:85461512-85464970	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:85464493-85464944	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
MCOLN2	TF binding region
WDR63	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10782534	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10782536	0.84[EUR][1000 genomes]
rs10873669	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10873670	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10873672	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873676	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873677	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873678	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10873679	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10873682	0.82[EUR][1000 genomes]
rs10873683	0.81[EUR][1000 genomes]
rs11161495	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11161496	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11161497	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11161498	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161499	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161501	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161502	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161503	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161504	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161505	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161513	0.82[EUR][1000 genomes]
rs11161514	0.81[EUR][1000 genomes]
rs11485283	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11485284	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11799517	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11804248	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12091131	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130357	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12138711	0.83[EUR][1000 genomes]
rs12730688	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12754569	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1439130	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1837328	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2389792	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389793	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2486755	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3850430	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3895846	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3904965	0.93[ASN][1000 genomes]
rs486751	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs488710	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4907017	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4907018	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4907118	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907125	0.81[EUR][1000 genomes]
rs495786	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs499539	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs513430	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs515303	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530486	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs531423	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs589653	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs600536	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603746	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs625045	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs631267	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs632545	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs648660	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs650529	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs651916	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6576736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs662948	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6677091	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685363	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs668860	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6691674	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691970	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6700622	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs677476	0.82[EUR][1000 genomes]
rs679167	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs726708	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720523	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7516329	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7516610	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516625	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519134	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522851	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541684	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7549346	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7552445	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7553886	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	esv3515392	chr1:85437980-85465392	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3515393	chr1:85437980-85465392	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3861690	MCOLN2	cis	Artery Aorta	GTEx
rs3861690	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs3861690	MCOLN2	cis	multi-tissue	Pritchard
rs3861690	MCOLN2	cis	Stomach	GTEx
rs3861690	MCOLN2	cis	Thyroid	GTEx
rs3861690	MCOLN2	cis	Artery Tibial	GTEx
rs3861690	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs3861690	MCOLN2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85461800-85464600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr1:85462000-85464600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:85462600-85464600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:85463000-85464600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
5	chr1:85463000-85464800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
6	chr1:85463000-85464800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:85463200-85464600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
8	chr1:85463200-85464800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
9	chr1:85463200-85464800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:85463400-85464600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:85463400-85464600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr1:85463400-85465000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr1:85463600-85464600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:85463600-85464600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
15	chr1:85463800-85464800	Bivalent/Poised TSS	NHEK	skin
16	chr1:85464000-85464600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:85464000-85464600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:85464000-85464600	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr1:85464000-85464600	Bivalent Enhancer	Placenta	Placenta
20	chr1:85464000-85464800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
21	chr1:85464000-85465000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:85464200-85464600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
23	chr1:85464200-85464600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
24	chr1:85464200-85464600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:85464200-85464600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr1:85464200-85464600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
27	chr1:85464200-85464600	Bivalent Enhancer	Fetal Intestine Small	intestine
28	chr1:85464200-85464600	Bivalent Enhancer	Thymus	Thymus
29	chr1:85464200-85464600	Bivalent Enhancer	NHDF-Ad	bronchial
30	chr1:85464200-85464800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:85464200-85464800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr1:85464200-85464800	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:85464200-85467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:85464400-85464600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
35	chr1:85464400-85464600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
36	chr1:85464400-85464600	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
37	chr1:85464400-85464600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr1:85464400-85464600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:85464400-85464600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:85464400-85464600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:85464400-85464600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
42	chr1:85464400-85464600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:85464400-85464600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
44	chr1:85464400-85464600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:85464400-85464600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:85464400-85464600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:85464400-85464600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:85464400-85464600	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr1:85464400-85464600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
50	chr1:85464400-85464800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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