Variant report

Variant	rs12646999
Chromosome Location	chr4:56754099-56754100
allele	C/G/T
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	RAD21	chr4:56753825-56754116	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:56754077-56754104	MCF-7	breast:	n/a	n/a
3	CTCF	chr4:56753837-56754112	K562	blood:	n/a	n/a
4	RFX5	chr4:56753595-56754345	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr4:56754000-56754150	GM12867	blood:	n/a	n/a
6	CTCF	chr4:56753846-56754110	GM12878	blood:	n/a	n/a
7	RAD21	chr4:56753788-56754186	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr4:56753960-56754110	GM12872	blood:	n/a	n/a

Variant related genes	Relation type
EXOC1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11658	0.82[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11722734	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12498449	0.97[ASN][1000 genomes]
rs17086129	0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs2290016	0.83[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs61260672	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6820052	0.97[ASN][1000 genomes]
rs73238374	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238378	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238385	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238389	0.97[ASN][1000 genomes]
rs73238391	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238392	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73238401	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv879024	chr4:56742205-56786589	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv879025	chr4:56742205-56808607	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12646999	MCOLN3	trans	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56720400-56764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:56720800-56761800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:56721600-56774600	Weak transcription	Fetal Heart	heart
4	chr4:56733200-56763000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:56733600-56763000	Weak transcription	Stomach Mucosa	stomach
6	chr4:56733800-56772200	Weak transcription	Hela-S3	cervix
7	chr4:56733800-56772800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr4:56734400-56773000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:56734600-56773400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:56735000-56768000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:56736000-56762400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:56737000-56774800	Weak transcription	Psoas Muscle	Psoas
13	chr4:56737600-56763400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:56738000-56771400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:56739800-56759800	Weak transcription	HMEC	breast
16	chr4:56745600-56760000	Weak transcription	Fetal Kidney	kidney
17	chr4:56745800-56757400	Weak transcription	Brain Substantia Nigra	brain
18	chr4:56745800-56757800	Weak transcription	Brain Germinal Matrix	brain
19	chr4:56745800-56759800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:56745800-56772800	Weak transcription	Small Intestine	intestine
21	chr4:56747400-56758800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:56747600-56756200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:56747800-56755000	Weak transcription	NHDF-Ad	bronchial
24	chr4:56747800-56759600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:56747800-56759800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:56747800-56760000	Weak transcription	Fetal Brain Male	brain
27	chr4:56747800-56772800	Weak transcription	NHEK	skin
28	chr4:56748000-56758600	Weak transcription	Fetal Brain Female	brain
29	chr4:56748000-56763400	Weak transcription	Brain Angular Gyrus	brain
30	chr4:56748000-56763800	Weak transcription	Esophagus	oesophagus
31	chr4:56748000-56770000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:56748000-56772000	Weak transcription	NHLF	lung
33	chr4:56748000-56773200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:56748200-56756000	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:56748200-56758800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:56748200-56759000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:56748200-56760000	Weak transcription	Spleen	Spleen
38	chr4:56748200-56762000	Weak transcription	HSMMtube	muscle
39	chr4:56748200-56773400	Weak transcription	Gastric	stomach
40	chr4:56748400-56759600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:56748400-56762600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:56748400-56765400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:56748400-56770200	Weak transcription	HepG2	liver
44	chr4:56748600-56754800	Weak transcription	Fetal Lung	lung
45	chr4:56748600-56755600	Weak transcription	Primary B cells from cord blood	blood
46	chr4:56748600-56755600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:56748600-56756000	Weak transcription	Brain Anterior Caudate	brain
48	chr4:56748600-56756000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:56748600-56756200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:56748600-56757200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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