Variant report

Variant	rs3213213
Chromosome Location	chr12:21674259-21674260
allele	C/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	POLR2A	chr12:21671064-21674732	K562	blood:	n/a	n/a
2	POLR2A	chr12:21673268-21674578	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21671832..21674785-chr12:21687913..21690095,2	K562	blood:
2	chr12:21654473..21659052-chr12:21670057..21674835,6	K562	blood:

Variant related genes	Relation type
C12orf39	TF binding region
ENSG00000004700	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1060126	1.00[CHD][hapmap]
rs1061626	1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061627	1.00[CHD][hapmap]
rs11046090	0.92[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046091	0.89[ASW][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs11046092	1.00[CEU][hapmap]
rs11046094	0.84[CEU][hapmap]
rs12312710	0.84[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];1.00[ASN][1000 genomes]
rs1558502	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16923862	0.92[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627102	0.84[CEU][hapmap]
rs3088178	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60206314	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61926330	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61926342	1.00[ASN][1000 genomes]
rs67187752	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299256	1.00[ASN][1000 genomes]
rs7307064	1.00[CHD][hapmap]
rs7310464	0.82[CEU][hapmap]
rs7313618	1.00[ASN][1000 genomes]
rs7965230	0.94[ASW][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7976409	1.00[CHD][hapmap]

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	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
6	nsv528556	chr12:21664879-21680363	Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv557743	chr12:21670410-21688900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3213213	PYROXD1	cis	cerebellum	SCAN
rs3213213	PYROXD1	cis	parietal	SCAN
rs3213213	RECQL	cis	cerebellum	SCAN
rs3213213	KCNJ8	cis	parietal	SCAN
rs3213213	GOLT1B	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21655400-21674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:21656000-21674600	Weak transcription	Fetal Kidney	kidney
3	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
4	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
5	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:21657600-21675000	Weak transcription	Small Intestine	intestine
8	chr12:21657600-21675400	Weak transcription	Fetal Brain Male	brain
9	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
10	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:21657600-21680400	Weak transcription	Gastric	stomach
12	chr12:21661400-21677200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:21666000-21680200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:21666800-21675800	Weak transcription	HepG2	liver
15	chr12:21666800-21676800	Weak transcription	Fetal Brain Female	brain
16	chr12:21666800-21679800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:21666800-21680000	Weak transcription	Psoas Muscle	Psoas
18	chr12:21666800-21680200	Weak transcription	Colonic Mucosa	Colon
19	chr12:21666800-21680400	Weak transcription	Spleen	Spleen
20	chr12:21667000-21674400	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:21667000-21675000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:21667000-21680200	Weak transcription	Left Ventricle	heart
23	chr12:21667000-21680200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:21667000-21680200	Weak transcription	HSMMtube	muscle
25	chr12:21667200-21678000	Weak transcription	Lung	lung
26	chr12:21667200-21680000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:21667200-21680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:21667200-21680000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:21667600-21680000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:21667600-21680200	Weak transcription	NHLF	lung
31	chr12:21669200-21675400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:21669200-21680000	Weak transcription	HMEC	breast
33	chr12:21669400-21675800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:21669400-21678200	Weak transcription	A549	lung
35	chr12:21669400-21678800	Weak transcription	Hela-S3	cervix
36	chr12:21669400-21679000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:21669400-21680200	Weak transcription	Placenta	Placenta
38	chr12:21669600-21675000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:21669600-21676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:21669800-21678000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:21669800-21679800	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:21670000-21675600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:21670000-21676600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:21670000-21678000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:21670200-21676400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:21670200-21680000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:21670400-21674400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:21670400-21674800	Weak transcription	HUVEC	blood vessel
49	chr12:21670400-21675400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:21670600-21674400	Weak transcription	Fetal Lung	lung

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