Variant report

Variant	rs12423412
Chromosome Location	chr12:21652641-21652642
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	chr12:21652633-21652833	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:21629758..21631544-chr12:21651304..21653537,2	MCF-7	breast:
2	chr12:21632020..21637029-chr12:21648453..21652691,4	K562	blood:
3	chr12:21635310..21637987-chr12:21651998..21654175,2	K562	blood:

Variant related genes	Relation type
GOLT1B	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1029931	0.88[CEU][hapmap]
rs10492117	0.83[CHD][hapmap]
rs10770819	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs10841833	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10841835	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10841837	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10841839	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs10841840	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs11046089	0.81[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11046093	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs11046098	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11046099	0.88[EUR][1000 genomes]
rs11046100	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs11046102	0.87[EUR][1000 genomes]
rs12231436	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12424924	0.87[CEU][hapmap]
rs12829302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12833589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17682462	0.86[CEU][hapmap]
rs2110159	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2159944	0.93[CEU][hapmap];0.81[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs2284393	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2284394	0.90[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs2284395	0.91[ASN][1000 genomes]
rs2300211	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2300212	0.91[ASN][1000 genomes]
rs4762834	0.81[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12423412	PYROXD1	cis	parietal	SCAN
rs12423412	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs12423412	PYROXD1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21611000-21652800	Weak transcription	Small Intestine	intestine
2	chr12:21611000-21653600	Weak transcription	Esophagus	oesophagus
3	chr12:21614800-21652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:21617000-21653000	Weak transcription	Colonic Mucosa	Colon
5	chr12:21636200-21652800	Weak transcription	K562	blood
6	chr12:21636400-21653400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:21636400-21653800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:21647800-21653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:21648000-21653400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:21648000-21653600	Weak transcription	Pancreas	Pancrea
11	chr12:21649400-21653200	Weak transcription	Ovary	ovary
12	chr12:21650400-21652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:21650600-21652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:21650800-21653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:21651000-21652800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:21651000-21652800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:21651000-21652800	Weak transcription	Psoas Muscle	Psoas
18	chr12:21651000-21653200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:21651000-21653200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:21651000-21653400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:21651000-21653400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:21651200-21652800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr12:21651200-21652800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:21651200-21652800	Weak transcription	Spleen	Spleen
25	chr12:21651400-21652800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:21651400-21652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:21651400-21652800	Weak transcription	Aorta	Aorta
28	chr12:21651400-21652800	Weak transcription	Right Ventricle	heart
29	chr12:21651400-21652800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:21651400-21652800	Weak transcription	Thymus	Thymus
31	chr12:21651400-21653000	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:21651400-21653200	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:21651400-21653600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:21651400-21653600	Weak transcription	Gastric	stomach
35	chr12:21651400-21653600	Weak transcription	Lung	lung
36	chr12:21651600-21652800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:21651600-21652800	Weak transcription	Brain Angular Gyrus	brain
38	chr12:21651600-21652800	Weak transcription	Brain Anterior Caudate	brain
39	chr12:21651600-21652800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:21651600-21652800	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:21651600-21653000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:21651600-21653000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:21651600-21653000	Weak transcription	Fetal Brain Male	brain
44	chr12:21651600-21653200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:21651600-21653200	Weak transcription	Liver	Liver
46	chr12:21651600-21653200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:21651600-21653200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr12:21651600-21653400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:21651600-21653400	Weak transcription	Fetal Intestine Large	intestine
50	chr12:21651600-21653400	Weak transcription	Fetal Stomach	stomach

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