Variant report

Variant	rs10023020
Chromosome Location	chr4:122724604-122724605
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	chr4:122720772..122725008-chr4:122725244..122729002,8	K562	blood:

Variant related genes	Relation type
ENSG00000123737	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10001889	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10004284	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10007956	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10013916	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10024820	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10024878	0.80[AFR][1000 genomes]
rs10028375	0.85[AFR][1000 genomes]
rs10084948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1048433	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098643	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11724322	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11732666	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11733882	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11734075	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12510839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13106764	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13108419	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13113421	0.90[AFR][1000 genomes]
rs13117282	0.80[AFR][1000 genomes]
rs13119055	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]
rs13127488	0.86[CHB][hapmap];0.87[JPT][hapmap];0.80[AFR][1000 genomes]
rs13128434	0.90[AFR][1000 genomes]
rs13130789	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13131003	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13133876	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13140070	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13143218	0.96[CHB][hapmap];0.87[JPT][hapmap]
rs13145213	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]
rs13151345	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13152701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs1507993	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17005256	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]
rs2271176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292232	0.82[CHB][hapmap]
rs28435300	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28522256	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28672860	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3217772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34445121	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35341163	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35495505	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805158	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3805161	0.82[CHB][hapmap]
rs3811742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075065	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4075066	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4240262	0.90[AFR][1000 genomes]
rs4240263	0.90[AFR][1000 genomes]
rs4240264	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4833232	0.90[AFR][1000 genomes]
rs4833233	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4833234	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4833235	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4833236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4833771	1.00[YRI][hapmap]
rs4833773	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4833775	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4833778	0.82[CHB][hapmap]
rs5004355	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67150579	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67775544	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811867	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822155	0.90[AFR][1000 genomes]
rs6830443	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845901	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7676867	0.85[AFR][1000 genomes]
rs769236	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7699289	0.90[AFR][1000 genomes]
rs884701	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs951974	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AFR][1000 genomes]
rs953691	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs966555	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9993206	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9995319	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9998785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999362	0.97[AMR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10023020	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs10023020	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122723000-122724800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:122723000-122725800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:122723000-122726200	Weak transcription	Spleen	Spleen
4	chr4:122723000-122729600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:122723000-122733400	Weak transcription	Pancreas	Pancrea
6	chr4:122723000-122743600	Weak transcription	Esophagus	oesophagus
7	chr4:122723000-122743600	Weak transcription	Small Intestine	intestine
8	chr4:122723000-122744200	Weak transcription	Gastric	stomach
9	chr4:122723000-122744600	Weak transcription	Aorta	Aorta
10	chr4:122723200-122725200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:122723200-122725200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:122723200-122725400	Weak transcription	Brain Angular Gyrus	brain
13	chr4:122723200-122725800	Weak transcription	Brain Substantia Nigra	brain
14	chr4:122723200-122729200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:122723200-122731400	Weak transcription	Right Ventricle	heart
16	chr4:122723200-122737000	Weak transcription	Colonic Mucosa	Colon
17	chr4:122723200-122741800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:122723200-122743400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:122723200-122743600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:122723200-122743800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:122723400-122724800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:122723400-122724800	Weak transcription	Fetal Stomach	stomach
23	chr4:122723400-122725000	Transcr. at gene 5' and 3'	Dnd41	blood
24	chr4:122723400-122725400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:122723400-122727200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:122723400-122729400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:122723400-122744200	Weak transcription	Stomach Mucosa	stomach
28	chr4:122723600-122724800	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:122723600-122725000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:122723600-122725000	Weak transcription	NHLF	lung
31	chr4:122723600-122725200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:122723600-122725600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:122723600-122725800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:122723600-122725800	Weak transcription	Brain Hippocampus Middle	brain
35	chr4:122723600-122725800	Weak transcription	Fetal Brain Female	brain
36	chr4:122723600-122725800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:122723600-122725800	Weak transcription	A549	lung
38	chr4:122723600-122726000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr4:122723600-122727600	Weak transcription	Fetal Brain Male	brain
40	chr4:122723600-122728800	Weak transcription	HUVEC	blood vessel
41	chr4:122723600-122732400	Weak transcription	Psoas Muscle	Psoas
42	chr4:122723600-122742200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:122723600-122742400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:122723600-122742800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:122723800-122725000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:122723800-122725400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:122723800-122725600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr4:122723800-122726600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:122723800-122727400	Strong transcription	Brain Germinal Matrix	brain
50	chr4:122723800-122733000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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