Variant report

Variant	rs1048433
Chromosome Location	chr4:122748996-122748997
allele	G/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	FOSL2	chr4:122748880-122749511	SK-N-SH	brain:	n/a	n/a
2	CEBPB	chr4:122748984-122749419	K562	blood:	n/a	n/a
3	JUN	chr4:122748617-122749428	K562	blood:	n/a	n/a
4	IRF1	chr4:122748859-122749432	K562	blood:	n/a	n/a
5	GATA2	chr4:122748974-122749410	K562	blood:	n/a	n/a
6	TEAD4	chr4:122748941-122749431	K562	blood:	n/a	n/a
7	TCF12	chr4:122748827-122749572	SK-N-SH	brain:	n/a	n/a
8	JUND	chr4:122748994-122749413	Hela-S3	cervix:	n/a	chr4:122749165-122749176
9	PBX3	chr4:122748906-122749398	SK-N-SH	brain:	n/a	n/a
10	PML	chr4:122748950-122749454	K562	blood:	n/a	n/a
11	EP300	chr4:122748854-122749478	SK-N-SH	brain:	n/a	n/a
12	JUND	chr4:122748984-122749469	SK-N-SH	brain:	n/a	chr4:122749165-122749176
13	FOSL2	chr4:122748930-122749401	SK-N-SH	brain:	n/a	n/a
14	GATA1	chr4:122748861-122749555	K562	blood:	n/a	chr4:122749092-122749103
15	JUND	chr4:122748925-122749483	SK-N-SH	brain:	n/a	chr4:122749165-122749176
16	GATA3	chr4:122748949-122749583	SK-N-SH	brain:	n/a	n/a
17	STAT5A	chr4:122748955-122749410	K562	blood:	n/a	n/a
18	ARID3A	chr4:122748536-122749521	K562	blood:	n/a	n/a
19	IRF1	chr4:122748817-122749495	K562	blood:	n/a	n/a
20	KAP1	chr4:122748849-122749357	K562	blood:	n/a	n/a
21	POLR2A	chr4:122748979-122749423	SK-N-SH	brain:	n/a	n/a
22	FOS	chr4:122748995-122749373	MCF10A-Er-Src	breast:	n/a	chr4:122749165-122749176
23	GATA3	chr4:122748829-122749620	SK-N-SH	brain:	n/a	n/a
24	PBX3	chr4:122748948-122749438	SK-N-SH	brain:	n/a	n/a
25	GATA2	chr4:122748958-122749425	HUVEC	blood vessel:	n/a	n/a
26	TCF12	chr4:122748840-122749595	SK-N-SH	brain:	n/a	n/a
27	JUND	chr4:122748850-122749450	SK-N-SH	brain:	n/a	chr4:122749165-122749176
28	E2F4	chr4:122748756-122749316	MCF10A-Er-Src	breast:	n/a	n/a
29	EP300	chr4:122748984-122749365	Hela-S3	cervix:	n/a	n/a
30	NFIC	chr4:122748884-122749485	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:122743548..122747768-chr4:122748127..122751699,7	K562	blood:
2	chr4:122743051..122746003-chr4:122747790..122749584,2	MCF-7	breast:

Variant related genes	Relation type
CCNA2	TF binding region
ENSG00000145386	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10001889	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10004284	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10007956	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10013916	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10023020	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]
rs10024820	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10024878	0.85[AFR][1000 genomes]
rs10028375	0.90[AFR][1000 genomes]
rs10084948	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098643	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11724322	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11732666	0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap]
rs11733882	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11734075	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12510839	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13106764	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13108419	0.95[AFR][1000 genomes]
rs13113421	0.95[AFR][1000 genomes]
rs13117282	0.84[AFR][1000 genomes]
rs13119055	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]
rs13127488	0.84[AFR][1000 genomes]
rs13128434	0.95[AFR][1000 genomes]
rs13130789	0.95[AFR][1000 genomes]
rs13131003	0.81[CHB][hapmap]
rs13133876	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs13140070	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13143218	0.82[CHB][hapmap]
rs13145213	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]
rs13145558	0.80[AFR][1000 genomes]
rs13151345	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap]
rs13152701	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs1507993	0.82[GIH][hapmap]
rs17005256	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271176	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292232	0.82[GIH][hapmap]
rs28435300	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28522256	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28672860	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3217772	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34445121	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35341163	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35495505	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762840	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];0.90[ASN][1000 genomes]
rs3805158	0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap]
rs3805161	0.82[GIH][hapmap]
rs3811742	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4075065	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4075066	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4240262	0.95[AFR][1000 genomes]
rs4240263	0.95[AFR][1000 genomes]
rs4240264	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4833232	0.95[AFR][1000 genomes]
rs4833234	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4833235	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4833236	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4833771	1.00[YRI][hapmap]
rs4833773	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4833775	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4833778	0.84[GIH][hapmap]
rs5004355	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67150579	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs67775544	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6811867	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6822155	0.95[AFR][1000 genomes]
rs6830443	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6845901	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7676867	0.90[AFR][1000 genomes]
rs769236	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7699289	0.95[AFR][1000 genomes]
rs884701	0.82[GIH][hapmap]
rs906496	0.82[GIH][hapmap]
rs951974	1.00[ASW][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.84[AFR][1000 genomes]
rs953691	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap]
rs966555	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9993206	1.00[ASW][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs9995319	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9998785	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9999362	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[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
rs1048433	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL
rs1048433	CCNA2	cis	lymphoblastoid	seeQTL
rs1048433	CCNA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 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	chr4:122745600-122749000	Weak transcription	NHLF	lung
10	chr4:122745600-122750400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:122745600-122750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:122745600-122750600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:122745600-122750600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:122745600-122750600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:122745600-122750600	Weak transcription	Left Ventricle	heart
16	chr4:122745600-122750800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:122745600-122751800	Weak transcription	Ovary	ovary
18	chr4:122745600-122758000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:122745600-122758600	Weak transcription	Fetal Kidney	kidney
20	chr4:122745600-122759800	Weak transcription	Fetal Thymus	thymus
21	chr4:122745600-122760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:122745600-122762000	Weak transcription	Aorta	Aorta
23	chr4:122745600-122764000	Weak transcription	Colonic Mucosa	Colon
24	chr4:122745600-122766200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:122745600-122766600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:122745600-122767200	Weak transcription	Esophagus	oesophagus
27	chr4:122745600-122767200	Weak transcription	Right Ventricle	heart
28	chr4:122745600-122767800	Weak transcription	Pancreas	Pancrea
29	chr4:122745600-122767800	Weak transcription	Thymus	Thymus
30	chr4:122745600-122769200	Weak transcription	Hela-S3	cervix
31	chr4:122745600-122770000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:122745600-122781600	Weak transcription	Placenta	Placenta
33	chr4:122745600-122790400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:122745600-122790600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:122745600-122790800	Weak transcription	Psoas Muscle	Psoas
36	chr4:122745800-122749000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:122745800-122750200	Weak transcription	Fetal Lung	lung
38	chr4:122745800-122750400	Weak transcription	Fetal Stomach	stomach
39	chr4:122745800-122750600	Weak transcription	Primary B cells from cord blood	blood
40	chr4:122745800-122750600	Weak transcription	Primary T cells from cord blood	blood
41	chr4:122745800-122750600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:122745800-122750600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:122745800-122750600	Weak transcription	NHEK	skin
44	chr4:122745800-122750800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:122745800-122750800	Weak transcription	Fetal Intestine Large	intestine
46	chr4:122745800-122750800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr4:122745800-122751200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:122745800-122752400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:122745800-122753000	Weak transcription	Brain Angular Gyrus	brain
50	chr4:122745800-122753200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links