Variant report

Variant	rs2300212
Chromosome Location	chr12:21653716-21653717
allele	A/C
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	chr12:21653554-21655298	PBDE	blood:	n/a	n/a
2	MXI1	chr12:21653059-21655687	SK-N-SH	brain:	n/a	n/a
3	NFYA	chr12:21653595-21655008	Hela-S3	cervix:	n/a	chr12:21654587-21654600 chr12:21654589-21654599 chr12:21654587-21654602 chr12:21654587-21654602 chr12:21654586-21654598 chr12:21654587-21654601
4	POLR2A	chr12:21653128-21655528	H1-hESC	embryonic stem cell:	n/a	n/a
5	USF2	chr12:21653712-21654799	Hela-S3	cervix:	n/a	n/a
6	CHD1	chr12:21653673-21654039	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:21653622-21655342	HUVEC	blood vessel:	n/a	n/a
8	RCOR1	chr12:21653713-21654874	K562	blood:	n/a	n/a
9	WRNIP1	chr12:21653546-21655305	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:21653680-21655402	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:21653368-21655463	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:21653401-21655462	GM19099	blood:	n/a	n/a
13	POLR2A	chr12:21653518-21655441	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:21653624-21653726	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:21653130-21656931	IMR90	lung:	n/a	n/a
16	POLR2A	chr12:21653519-21655398	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr12:21653715-21655502	NB4	blood:	n/a	chr12:21654901-21654911
18	POLR2A	chr12:21653306-21656829	HepG2	liver:	n/a	n/a
19	MXI1	chr12:21653094-21655605	IMR90	lung:	n/a	n/a
20	POLR2A	chr12:21653418-21656273	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:21653363-21655706	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21653197..21655257-chr12:21809726..21811694,2	K562	blood:
2	chr12:21635310..21637987-chr12:21651998..21654175,2	K562	blood:

Variant related genes	Relation type
GOLT1B	TF binding region
ENSG00000111716	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10492117	0.81[ASN][1000 genomes]
rs10841835	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10841836	0.81[ASN][1000 genomes]
rs11046089	0.83[ASN][1000 genomes]
rs12231436	0.91[ASN][1000 genomes]
rs12423412	0.91[ASN][1000 genomes]
rs12822436	0.83[ASN][1000 genomes]
rs12829302	0.91[ASN][1000 genomes]
rs12833589	0.91[ASN][1000 genomes]
rs2110159	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2284393	0.86[ASN][1000 genomes]
rs2284394	0.98[ASN][1000 genomes]
rs2284395	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2300211	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417991	0.81[ASN][1000 genomes]
rs34965831	0.83[ASN][1000 genomes]
rs3782661	0.82[ASN][1000 genomes]
rs4762834	0.83[ASN][1000 genomes]
rs4762835	0.83[ASN][1000 genomes]
rs61926332	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2300212	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs2300212	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs2300212	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2300212	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21636400-21653800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:21650800-21653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:21652200-21653800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:21652600-21653800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:21652600-21653800	Flanking Active TSS	NH-A	brain
6	chr12:21652600-21654000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:21652600-21654000	Flanking Active TSS	Osteobl	bone
8	chr12:21652600-21654200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:21652600-21656200	Active TSS	NHLF	lung
10	chr12:21652800-21653800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr12:21652800-21653800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:21652800-21653800	Enhancers	Aorta	Aorta
13	chr12:21652800-21653800	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr12:21652800-21654000	Enhancers	Small Intestine	intestine
15	chr12:21652800-21654000	Enhancers	Spleen	Spleen
16	chr12:21652800-21654000	Flanking Active TSS	Dnd41	blood
17	chr12:21652800-21654000	Flanking Active TSS	Hela-S3	cervix
18	chr12:21652800-21654000	Flanking Active TSS	HMEC	breast
19	chr12:21652800-21654000	Flanking Active TSS	HUVEC	blood vessel
20	chr12:21652800-21655800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr12:21652800-21656000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:21652800-21656000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:21652800-21656000	Active TSS	Right Atrium	heart
24	chr12:21652800-21656400	Active TSS	Psoas Muscle	Psoas
25	chr12:21653000-21653800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:21653000-21654000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:21653000-21654000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr12:21653000-21654200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr12:21653000-21655800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:21653000-21656000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:21653000-21656000	Active TSS	Right Ventricle	heart
32	chr12:21653000-21656000	Active TSS	K562	blood
33	chr12:21653000-21656200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:21653000-21656200	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:21653200-21653800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr12:21653200-21653800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:21653200-21653800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:21653200-21653800	Flanking Active TSS	A549	lung
39	chr12:21653200-21653800	Flanking Active TSS	HSMMtube	muscle
40	chr12:21653200-21654000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:21653200-21654000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:21653200-21654000	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr12:21653200-21654000	Flanking Active TSS	Thymus	Thymus
44	chr12:21653200-21654200	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr12:21653200-21654200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr12:21653200-21654200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr12:21653200-21654200	Flanking Active TSS	Fetal Brain Female	brain
48	chr12:21653200-21654200	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr12:21653200-21654400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr12:21653200-21655400	Active TSS	Fetal Kidney	kidney

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