Variant report

Variant	rs10024820
Chromosome Location	chr4:122781402-122781403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FAM48A	chr4:122781336-122781414	GM12878	blood:	n/a	n/a
2	FOS	chr4:122781353-122781656	HUVEC	blood vessel:	n/a	n/a

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

Variant related genes	Relation type
BBS7	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10001889	0.95[ASN][1000 genomes]
rs10004284	0.95[ASN][1000 genomes]
rs10007956	0.95[ASN][1000 genomes]
rs10013916	0.95[ASN][1000 genomes]
rs10023020	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10084948	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048433	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098643	0.95[ASN][1000 genomes]
rs11724322	0.94[ASN][1000 genomes]
rs11732666	0.81[ASN][1000 genomes]
rs11733882	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734075	0.92[ASN][1000 genomes]
rs12510839	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106764	0.95[ASN][1000 genomes]
rs13108360	0.81[ASN][1000 genomes]
rs13119055	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121963	0.81[ASN][1000 genomes]
rs13130789	0.88[ASN][1000 genomes]
rs13133876	0.81[ASN][1000 genomes]
rs13138774	0.80[ASN][1000 genomes]
rs13140070	0.96[ASN][1000 genomes]
rs13143218	0.81[ASN][1000 genomes]
rs13145213	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13152701	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17005256	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271176	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28435300	0.96[ASN][1000 genomes]
rs28522256	0.96[ASN][1000 genomes]
rs28672860	0.96[ASN][1000 genomes]
rs3217772	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34445121	0.96[ASN][1000 genomes]
rs35341163	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35495505	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762840	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805158	0.80[ASN][1000 genomes]
rs3811742	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4833233	0.88[ASN][1000 genomes]
rs4833234	0.92[ASN][1000 genomes]
rs4833235	0.92[ASN][1000 genomes]
rs4833236	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833773	0.88[ASN][1000 genomes]
rs4833775	0.96[ASN][1000 genomes]
rs4833777	0.81[ASN][1000 genomes]
rs5004355	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67150579	0.96[ASN][1000 genomes]
rs67775544	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6811867	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6830443	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6845901	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769236	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966555	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9995319	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998785	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9999362	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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
rs10024820	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL
rs10024820	CCNA2	Cis_1M	lymphoblastoid	RTeQTL

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	chr4:122762800-122790200	Weak transcription	Brain Substantia Nigra	brain
24	chr4:122764600-122790600	Weak transcription	Colonic Mucosa	Colon
25	chr4:122768000-122781800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:122768000-122787000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:122768000-122790000	Weak transcription	Fetal Brain Male	brain
28	chr4:122768000-122790600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:122768000-122790600	Weak transcription	Right Ventricle	heart
30	chr4:122768200-122783800	Weak transcription	Pancreas	Pancrea
31	chr4:122768200-122790200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:122768200-122790600	Weak transcription	Esophagus	oesophagus
33	chr4:122768200-122790600	Weak transcription	HSMMtube	muscle
34	chr4:122768200-122790800	Weak transcription	Aorta	Aorta
35	chr4:122768200-122790800	Weak transcription	Gastric	stomach
36	chr4:122768400-122781800	Weak transcription	Liver	Liver
37	chr4:122768800-122781600	Weak transcription	Dnd41	blood
38	chr4:122768800-122786600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:122768800-122790200	Weak transcription	Fetal Kidney	kidney
40	chr4:122770600-122781600	Weak transcription	Adipose Nuclei	Adipose
41	chr4:122770600-122781600	Weak transcription	NHLF	lung
42	chr4:122770600-122786600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:122770600-122787400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:122770600-122790200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:122770600-122790600	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:122770800-122781800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:122770800-122783600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr4:122770800-122783800	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:122771000-122783800	Weak transcription	Left Ventricle	heart
50	chr4:122771000-122790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links