Variant report

Variant	rs62246183
Chromosome Location	chr3:46720260-46720261
allele	C/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	RAD21	chr3:46720173-46720333	H1-hESC	embryonic stem cell:	n/a	chr3:46720207-46720221 chr3:46720211-46720223
2	CTCF	chr3:46720164-46720270	H1-hESC	embryonic stem cell:	n/a	n/a
3	BATF	chr3:46720127-46720375	GM12878	blood:	n/a	n/a
4	MAX	chr3:46719856-46720396	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr3:46720185-46720372	H1-hESC	embryonic stem cell:	n/a	n/a
6	BATF	chr3:46720130-46720422	GM12878	blood:	n/a	n/a
7	CTCF	chr3:46720199-46720265	GM12892	blood:	n/a	n/a
8	E2F6	chr3:46719698-46720447	H1-hESC	embryonic stem cell:	n/a	chr3:46719995-46720007 chr3:46719930-46719939
9	E2F6	chr3:46719804-46720337	H1-hESC	embryonic stem cell:	n/a	chr3:46719995-46720007 chr3:46719930-46719939

No.	Distal block	Cell Line	Cell type
1	chr3:46720178..46722487-chr3:46787613..46789601,2	K562	blood:
2	chr3:46703743..46706705-chr3:46719567..46721829,2	K562	blood:
3	chr3:46719842..46724126-chr3:46725182..46728551,5	MCF-7	breast:

Variant related genes	Relation type
ALS2CL	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11711074	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12496585	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3210183	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34190208	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3935248	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682825	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55991232	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56069285	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56670151	0.82[ASN][1000 genomes]
rs61277784	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792255	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7372799	0.81[AMR][1000 genomes]
rs7373358	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7426833	0.81[AMR][1000 genomes]
rs7613489	0.81[AMR][1000 genomes]
rs7615747	0.81[AMR][1000 genomes]
rs7625303	0.84[EUR][1000 genomes]
rs7633016	0.81[AMR][1000 genomes]
rs7634963	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7642448	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1804680	chr3:46704348-46869911	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv876742	chr3:46705369-46763839	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	nsv536555	chr3:46706571-46817963	Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv536556	chr3:46706571-46849443	Genic enhancers Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv536557	chr3:46706571-46853434	Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv10268	chr3:46707169-46736718	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	esv1797503	chr3:46708712-46760713	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
17	nsv876743	chr3:46716523-46753577	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
18	nsv876744	chr3:46716523-46763839	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62246183	ALS2CL	cis	Muscle Skeletal	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46702800-46732400	Weak transcription	Psoas Muscle	Psoas
2	chr3:46703000-46731600	Weak transcription	Hela-S3	cervix
3	chr3:46705400-46732600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:46705400-46734400	Weak transcription	Ovary	ovary
5	chr3:46710000-46722000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:46710200-46722800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:46711400-46726800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:46711400-46730400	Strong transcription	Primary T cells from cord blood	blood
9	chr3:46711400-46731800	Strong transcription	NHEK	skin
10	chr3:46711600-46731000	Strong transcription	Esophagus	oesophagus
11	chr3:46711800-46731200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:46712000-46720400	Strong transcription	Lung	lung
13	chr3:46712400-46730600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:46713000-46732000	Weak transcription	Stomach Mucosa	stomach
15	chr3:46714800-46729600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:46714800-46730400	Strong transcription	HMEC	breast
17	chr3:46715200-46723800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:46715400-46731600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:46715600-46721800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:46715800-46724000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:46716000-46732000	Strong transcription	Fetal Intestine Small	intestine
22	chr3:46717200-46721400	Weak transcription	Pancreas	Pancrea
23	chr3:46717200-46723800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:46717400-46733800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:46717800-46722000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:46717800-46722400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:46717800-46722400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:46717800-46722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:46717800-46722600	Weak transcription	Brain Substantia Nigra	brain
30	chr3:46717800-46733600	Weak transcription	Brain Angular Gyrus	brain
31	chr3:46717800-46734000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:46718000-46721000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:46718000-46721600	Weak transcription	Adipose Nuclei	Adipose
34	chr3:46718200-46720400	Weak transcription	Gastric	stomach
35	chr3:46718200-46720600	Weak transcription	Right Ventricle	heart
36	chr3:46718200-46723600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:46718600-46722800	Weak transcription	Liver	Liver
38	chr3:46718600-46724200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:46718800-46720600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:46718800-46721400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:46718800-46721600	Weak transcription	Colonic Mucosa	Colon
42	chr3:46718800-46722000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:46719000-46721400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:46719200-46720600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:46719200-46721000	Strong transcription	Placenta	Placenta
46	chr3:46719200-46721800	Weak transcription	Left Ventricle	heart
47	chr3:46719200-46722600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:46719200-46723200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:46719200-46724400	Weak transcription	Fetal Stomach	stomach
50	chr3:46719200-46732000	Weak transcription	Right Atrium	heart

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