Variant report

Variant	rs13119055
Chromosome Location	chr4:122755162-122755163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:122745006..122746599-chr4:122752412..122755944,3	K562	blood:

Variant related genes	Relation type
ENSG00000145386	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10001889	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10004284	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10007956	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10013916	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10023020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10024820	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10024878	0.89[AFR][1000 genomes]
rs10028375	0.95[AFR][1000 genomes]
rs10084948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1048433	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11098643	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11724322	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11732666	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs11733882	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734075	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12510839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13106764	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13108360	0.82[ASN][1000 genomes]
rs13108419	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13113338	0.80[AFR][1000 genomes]
rs13113421	1.00[AFR][1000 genomes]
rs13117282	0.89[AFR][1000 genomes]
rs13119958	0.80[ASN][1000 genomes]
rs13121963	0.82[ASN][1000 genomes]
rs13127488	0.86[CHB][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13128434	1.00[AFR][1000 genomes]
rs13130789	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13131003	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs13133876	0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs13138774	0.81[ASN][1000 genomes]
rs13140070	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13143218	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs13145213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145558	0.85[AFR][1000 genomes]
rs13151345	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs13152701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507993	0.86[CHB][hapmap]
rs17005256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292232	0.81[CHB][hapmap]
rs28435300	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28522256	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28672860	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3217772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34445121	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35341163	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35495505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805158	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs3805161	0.81[CHB][hapmap]
rs3811742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4075065	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4075066	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4240262	1.00[AFR][1000 genomes]
rs4240263	1.00[AFR][1000 genomes]
rs4240264	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4833232	1.00[AFR][1000 genomes]
rs4833233	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4833234	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4833235	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4833236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4833771	1.00[YRI][hapmap]
rs4833773	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4833775	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4833777	0.81[ASN][1000 genomes]
rs4833778	0.81[CHB][hapmap]
rs5004355	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67150579	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs67775544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811867	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6822155	1.00[AFR][1000 genomes]
rs6828650	0.80[AFR][1000 genomes]
rs6830443	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845901	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7676867	0.95[AFR][1000 genomes]
rs769236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699289	1.00[AFR][1000 genomes]
rs884701	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs951974	0.91[CHB][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs953691	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs966555	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9993206	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9995319	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9998785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999362	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13119055	CCNA2	cis	multi-tissue	Pritchard
rs13119055	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs13119055	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122745400-122767200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:122745400-122777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:122745400-122790400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:122745400-122790600	Weak transcription	Small Intestine	intestine
5	chr4:122745600-122758000	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:122745600-122758600	Weak transcription	Fetal Kidney	kidney
7	chr4:122745600-122759800	Weak transcription	Fetal Thymus	thymus
8	chr4:122745600-122760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:122745600-122762000	Weak transcription	Aorta	Aorta
10	chr4:122745600-122764000	Weak transcription	Colonic Mucosa	Colon
11	chr4:122745600-122766200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:122745600-122766600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:122745600-122767200	Weak transcription	Esophagus	oesophagus
14	chr4:122745600-122767200	Weak transcription	Right Ventricle	heart
15	chr4:122745600-122767800	Weak transcription	Pancreas	Pancrea
16	chr4:122745600-122767800	Weak transcription	Thymus	Thymus
17	chr4:122745600-122769200	Weak transcription	Hela-S3	cervix
18	chr4:122745600-122770000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:122745600-122781600	Weak transcription	Placenta	Placenta
20	chr4:122745600-122790400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:122745600-122790600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:122745600-122790800	Weak transcription	Psoas Muscle	Psoas
23	chr4:122745800-122758000	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:122745800-122758400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:122745800-122758800	Weak transcription	HUVEC	blood vessel
26	chr4:122745800-122759800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:122745800-122761600	Weak transcription	Brain Substantia Nigra	brain
28	chr4:122745800-122764000	Weak transcription	Brain Hippocampus Middle	brain
29	chr4:122745800-122765600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr4:122745800-122765600	Weak transcription	Fetal Heart	heart
31	chr4:122745800-122766600	Weak transcription	Fetal Brain Male	brain
32	chr4:122745800-122766600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:122745800-122766800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:122745800-122767200	Weak transcription	HSMMtube	muscle
35	chr4:122745800-122767400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:122745800-122768600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:122745800-122770200	Weak transcription	GM12878-XiMat	blood
38	chr4:122745800-122772000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:122745800-122779200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr4:122745800-122781200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:122745800-122786800	Weak transcription	A549	lung
42	chr4:122745800-122790200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:122745800-122790400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:122745800-122790400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:122745800-122790400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:122745800-122790800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:122747400-122761000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:122748000-122756600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:122748400-122762800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:122749200-122764600	Weak transcription	NH-A	brain

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