Variant report

Variant	rs2300211
Chromosome Location	chr12:21653119-21653120
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	MXI1	chr12:21653059-21655687	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:21653091-21653291	MCF10A-Er-Src	breast:	n/a	n/a
3	E2F4	chr12:21653043-21653398	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr12:21653094-21655605	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21629758..21631544-chr12:21651304..21653537,2	MCF-7	breast:
2	chr12:21635310..21637987-chr12:21651998..21654175,2	K562	blood:

Variant related genes	Relation type
GOLT1B	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10492117	0.81[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1061627	0.88[ASW][hapmap]
rs10770819	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs10841833	0.82[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs10841835	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10841836	0.81[ASN][1000 genomes]
rs10841837	0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs10841839	0.82[CHB][hapmap]
rs10841840	0.82[CHB][hapmap]
rs11046089	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs11046093	0.81[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11046098	0.82[CHB][hapmap]
rs12231436	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12423412	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12822436	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12829302	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12833589	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2110159	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2284393	0.88[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2284394	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2284395	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2300212	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417991	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs34965831	0.83[ASN][1000 genomes]
rs3782661	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4762834	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4762835	0.84[JPT][hapmap];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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2300211	PYROXD1	cis	cerebellum	SCAN
rs2300211	PYROXD1	cis	parietal	SCAN
rs2300211	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2300211	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs2300211	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2300211	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs2300211	RECQL	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21611000-21653600	Weak transcription	Esophagus	oesophagus
2	chr12:21636400-21653400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:21636400-21653800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:21647800-21653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:21648000-21653400	Weak transcription	Fetal Intestine Small	intestine
6	chr12:21648000-21653600	Weak transcription	Pancreas	Pancrea
7	chr12:21649400-21653200	Weak transcription	Ovary	ovary
8	chr12:21650800-21653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:21651000-21653200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:21651000-21653200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:21651000-21653400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:21651000-21653400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:21651400-21653200	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:21651400-21653600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:21651400-21653600	Weak transcription	Gastric	stomach
16	chr12:21651400-21653600	Weak transcription	Lung	lung
17	chr12:21651600-21653200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:21651600-21653200	Weak transcription	Liver	Liver
19	chr12:21651600-21653200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:21651600-21653200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:21651600-21653400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:21651600-21653400	Weak transcription	Fetal Intestine Large	intestine
23	chr12:21651600-21653400	Weak transcription	Fetal Stomach	stomach
24	chr12:21651600-21653400	Weak transcription	Fetal Thymus	thymus
25	chr12:21651600-21653600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:21651600-21653600	Weak transcription	Left Ventricle	heart
27	chr12:21651600-21653600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:21651800-21653200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:21651800-21653200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:21651800-21653600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:21652000-21653200	Enhancers	Fetal Brain Female	brain
32	chr12:21652000-21653400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr12:21652000-21653600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr12:21652200-21653200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:21652200-21653400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:21652200-21653800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:21652400-21653200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:21652400-21653200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:21652400-21653200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr12:21652400-21653200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:21652400-21653400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:21652400-21653400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr12:21652400-21653400	Weak transcription	Placenta	Placenta
44	chr12:21652600-21653200	Enhancers	Primary B cells from cord blood	blood
45	chr12:21652600-21653200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr12:21652600-21653200	Enhancers	Fetal Kidney	kidney
47	chr12:21652600-21653200	Active TSS	A549	lung
48	chr12:21652600-21653200	Enhancers	HepG2	liver
49	chr12:21652600-21653400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:21652600-21653400	Enhancers	Cortex derived primary cultured neurospheres	brain

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