Variant report

Variant	rs12499222
Chromosome Location	chr4:122774917-122774918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:122773768..122776743-chr4:122779512..122783185,3	K562	blood:
2	chr4:122765533..122767620-chr4:122774008..122775927,2	K562	blood:

Variant related genes	Relation type
ENSG00000138686	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10024445	0.88[ASN][1000 genomes]
rs11098647	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11726779	0.88[ASN][1000 genomes]
rs11732582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13105974	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13106485	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1532968	0.88[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17517624	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs2661553	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2661555	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2706791	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2706792	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2706793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2706796	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4295291	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4995894	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap]
rs6534321	0.90[ASN][1000 genomes]
rs6534325	0.95[ASN][1000 genomes]
rs6815050	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6835864	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838198	0.88[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6841843	0.83[CEU][hapmap]
rs7672640	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7690095	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9999982	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer 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	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12499222	CCNA2	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122745400-122777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:122745400-122790400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:122745400-122790600	Weak transcription	Small Intestine	intestine
4	chr4:122745600-122781600	Weak transcription	Placenta	Placenta
5	chr4:122745600-122790400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:122745600-122790600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:122745600-122790800	Weak transcription	Psoas Muscle	Psoas
8	chr4:122745800-122779200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:122745800-122781200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:122745800-122786800	Weak transcription	A549	lung
11	chr4:122745800-122790200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:122745800-122790400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:122745800-122790400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:122745800-122790400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:122745800-122790800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:122751400-122789800	Weak transcription	NHEK	skin
17	chr4:122751400-122790400	Weak transcription	Primary B cells from cord blood	blood
18	chr4:122751600-122790200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:122754000-122778200	Weak transcription	Lung	lung
20	chr4:122754600-122790000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:122755400-122790800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:122757600-122790200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:122758000-122790000	Weak transcription	HepG2	liver
24	chr4:122760600-122791000	Weak transcription	Spleen	Spleen
25	chr4:122761000-122785000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:122761200-122785000	Weak transcription	K562	blood
27	chr4:122761800-122781400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:122762800-122790200	Weak transcription	Brain Substantia Nigra	brain
29	chr4:122764600-122790600	Weak transcription	Colonic Mucosa	Colon
30	chr4:122765000-122781200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:122765000-122781400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:122767400-122781400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:122768000-122781400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:122768000-122781800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:122768000-122787000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:122768000-122790000	Weak transcription	Fetal Brain Male	brain
37	chr4:122768000-122790600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:122768000-122790600	Weak transcription	Right Ventricle	heart
39	chr4:122768200-122777800	Weak transcription	Thymus	Thymus
40	chr4:122768200-122778800	Weak transcription	Primary T cells from cord blood	blood
41	chr4:122768200-122779200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:122768200-122779200	Weak transcription	HSMM	muscle
43	chr4:122768200-122779400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:122768200-122780200	Weak transcription	HUVEC	blood vessel
45	chr4:122768200-122783800	Weak transcription	Pancreas	Pancrea
46	chr4:122768200-122790200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:122768200-122790600	Weak transcription	Esophagus	oesophagus
48	chr4:122768200-122790600	Weak transcription	HSMMtube	muscle
49	chr4:122768200-122790800	Weak transcription	Aorta	Aorta
50	chr4:122768200-122790800	Weak transcription	Gastric	stomach

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