Variant report

Variant	rs13145213
Chromosome Location	chr4:122750079-122750080
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	chr4:122743548..122747768-chr4:122748127..122751699,7	K562	blood:

Variant related genes	Relation type
ENSG00000145386	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10001889	0.96[ASN][1000 genomes]
rs10004284	0.96[ASN][1000 genomes]
rs10007956	0.96[ASN][1000 genomes]
rs10013916	0.96[ASN][1000 genomes]
rs10023020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10024820	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10084948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1048433	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11098643	0.96[ASN][1000 genomes]
rs11721457	0.82[CHB][hapmap]
rs11724322	0.95[ASN][1000 genomes]
rs11732666	0.95[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs11733882	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734075	0.93[ASN][1000 genomes]
rs12510839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13106764	0.96[ASN][1000 genomes]
rs13108360	0.82[ASN][1000 genomes]
rs13108419	0.80[ASN][1000 genomes]
rs13119055	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]
rs13119958	0.80[ASN][1000 genomes]
rs13121963	0.82[ASN][1000 genomes]
rs13127488	0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs13130789	0.88[ASN][1000 genomes]
rs13131003	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs13133876	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs13138774	0.81[ASN][1000 genomes]
rs13140070	0.97[ASN][1000 genomes]
rs13143218	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs13151345	0.95[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs13152701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507993	0.86[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs17005256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292232	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs28435300	0.97[ASN][1000 genomes]
rs28522256	0.97[ASN][1000 genomes]
rs28672860	0.97[ASN][1000 genomes]
rs3217772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34445121	0.97[ASN][1000 genomes]
rs35341163	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35495505	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805158	0.95[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs3805161	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs3811742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41462746	0.83[LWK][hapmap];0.88[YRI][hapmap]
rs4256243	0.83[LWK][hapmap];0.88[YRI][hapmap]
rs4833233	0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4833234	0.93[ASN][1000 genomes]
rs4833235	0.93[ASN][1000 genomes]
rs4833236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4833773	0.89[ASN][1000 genomes]
rs4833775	0.97[ASN][1000 genomes]
rs4833777	0.81[ASN][1000 genomes]
rs4833778	0.82[CHB][hapmap];0.84[GIH][hapmap]
rs5004355	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67150579	0.97[ASN][1000 genomes]
rs67775544	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811867	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6830443	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845901	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs769236	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884701	0.91[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs906496	0.83[GIH][hapmap]
rs951974	0.91[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.80[ASN][1000 genomes]
rs953691	0.95[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs966555	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995319	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9998785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999362	0.97[AFR][1000 genomes];0.98[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13145213	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL
rs13145213	EXOSC9	cis	lymphoblastoid	seeQTL
rs13145213	CCNA2	cis	lymphoblastoid	seeQTL
rs13145213	BBS7	cis	parietal	SCAN
rs13145213	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs13145213	BBS7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122745400-122750600	Weak transcription	Gastric	stomach
2	chr4:122745400-122750600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:122745400-122751200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:122745400-122753200	Weak transcription	Lung	lung
5	chr4:122745400-122767200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:122745400-122777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:122745400-122790400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:122745400-122790600	Weak transcription	Small Intestine	intestine
9	chr4:122745600-122750400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:122745600-122750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:122745600-122750600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:122745600-122750600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:122745600-122750600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:122745600-122750600	Weak transcription	Left Ventricle	heart
15	chr4:122745600-122750800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:122745600-122751800	Weak transcription	Ovary	ovary
17	chr4:122745600-122758000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:122745600-122758600	Weak transcription	Fetal Kidney	kidney
19	chr4:122745600-122759800	Weak transcription	Fetal Thymus	thymus
20	chr4:122745600-122760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:122745600-122762000	Weak transcription	Aorta	Aorta
22	chr4:122745600-122764000	Weak transcription	Colonic Mucosa	Colon
23	chr4:122745600-122766200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:122745600-122766600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:122745600-122767200	Weak transcription	Esophagus	oesophagus
26	chr4:122745600-122767200	Weak transcription	Right Ventricle	heart
27	chr4:122745600-122767800	Weak transcription	Pancreas	Pancrea
28	chr4:122745600-122767800	Weak transcription	Thymus	Thymus
29	chr4:122745600-122769200	Weak transcription	Hela-S3	cervix
30	chr4:122745600-122770000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:122745600-122781600	Weak transcription	Placenta	Placenta
32	chr4:122745600-122790400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:122745600-122790600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:122745600-122790800	Weak transcription	Psoas Muscle	Psoas
35	chr4:122745800-122750200	Weak transcription	Fetal Lung	lung
36	chr4:122745800-122750400	Weak transcription	Fetal Stomach	stomach
37	chr4:122745800-122750600	Weak transcription	Primary B cells from cord blood	blood
38	chr4:122745800-122750600	Weak transcription	Primary T cells from cord blood	blood
39	chr4:122745800-122750600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:122745800-122750600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:122745800-122750600	Weak transcription	NHEK	skin
42	chr4:122745800-122750800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:122745800-122750800	Weak transcription	Fetal Intestine Large	intestine
44	chr4:122745800-122750800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr4:122745800-122751200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:122745800-122752400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:122745800-122753000	Weak transcription	Brain Angular Gyrus	brain
48	chr4:122745800-122753200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr4:122745800-122753200	Weak transcription	Liver	Liver
50	chr4:122745800-122753800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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