Variant report

Variant	rs6838198
Chromosome Location	chr4:122781263-122781264
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:122775243..122777895-chr4:122780430..122781968,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10002280	0.99[ASN][1000 genomes]
rs10857086	0.99[ASN][1000 genomes]
rs11098647	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11732582	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs12499222	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]
rs13105974	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13106485	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1532968	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517624	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2661553	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2661555	0.88[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2706791	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2706792	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2706793	0.88[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2706796	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28665553	0.99[ASN][1000 genomes]
rs4295291	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4519820	0.99[ASN][1000 genomes]
rs4833774	0.99[ASN][1000 genomes]
rs4995894	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs6815050	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs6819870	0.99[ASN][1000 genomes]
rs6823686	0.92[ASN][1000 genomes]
rs6830128	0.97[ASN][1000 genomes]
rs6835864	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6836290	0.99[ASN][1000 genomes]
rs7661641	0.94[ASN][1000 genomes]
rs7672640	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7690095	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9999982	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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
rs6838198	CCNA2	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122745400-122790400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:122745400-122790600	Weak transcription	Small Intestine	intestine
3	chr4:122745600-122781600	Weak transcription	Placenta	Placenta
4	chr4:122745600-122790400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:122745600-122790600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:122745600-122790800	Weak transcription	Psoas Muscle	Psoas
7	chr4:122745800-122786800	Weak transcription	A549	lung
8	chr4:122745800-122790200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:122745800-122790400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:122745800-122790400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:122745800-122790400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:122745800-122790800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:122751400-122789800	Weak transcription	NHEK	skin
14	chr4:122751400-122790400	Weak transcription	Primary B cells from cord blood	blood
15	chr4:122751600-122790200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:122754600-122790000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:122755400-122790800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:122757600-122790200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:122758000-122790000	Weak transcription	HepG2	liver
20	chr4:122760600-122791000	Weak transcription	Spleen	Spleen
21	chr4:122761000-122785000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:122761200-122785000	Weak transcription	K562	blood
23	chr4:122761800-122781400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:122762800-122790200	Weak transcription	Brain Substantia Nigra	brain
25	chr4:122764600-122790600	Weak transcription	Colonic Mucosa	Colon
26	chr4:122765000-122781400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:122767400-122781400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:122768000-122781400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:122768000-122781800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:122768000-122787000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:122768000-122790000	Weak transcription	Fetal Brain Male	brain
32	chr4:122768000-122790600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:122768000-122790600	Weak transcription	Right Ventricle	heart
34	chr4:122768200-122783800	Weak transcription	Pancreas	Pancrea
35	chr4:122768200-122790200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:122768200-122790600	Weak transcription	Esophagus	oesophagus
37	chr4:122768200-122790600	Weak transcription	HSMMtube	muscle
38	chr4:122768200-122790800	Weak transcription	Aorta	Aorta
39	chr4:122768200-122790800	Weak transcription	Gastric	stomach
40	chr4:122768400-122781800	Weak transcription	Liver	Liver
41	chr4:122768600-122781400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:122768800-122781400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr4:122768800-122781600	Weak transcription	Dnd41	blood
44	chr4:122768800-122786600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:122768800-122790200	Weak transcription	Fetal Kidney	kidney
46	chr4:122769000-122781400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:122770400-122781400	Weak transcription	NH-A	brain
48	chr4:122770600-122781600	Weak transcription	Adipose Nuclei	Adipose
49	chr4:122770600-122781600	Weak transcription	NHLF	lung
50	chr4:122770600-122786600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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