Variant report

Variant	rs10753416
Chromosome Location	chr1:226410949-226410950
allele	C/G
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	RAD21	chr1:226410870-226411047	HepG2	liver:	n/a	n/a
2	CHD2	chr1:226410855-226411344	HepG2	liver:	n/a	n/a
3	RCOR1	chr1:226410813-226411424	HepG2	liver:	n/a	n/a
4	SRF	chr1:226410816-226411185	HepG2	liver:	n/a	chr1:226410972-226410990 chr1:226410974-226410987 chr1:226410975-226410992 chr1:226410972-226410986 chr1:226410976-226410990 chr1:226410970-226410988
5	ARID3A	chr1:226410737-226411118	HepG2	liver:	n/a	n/a
6	MYBL2	chr1:226410756-226411531	HepG2	liver:	n/a	n/a
7	BHLHE40	chr1:226410854-226411899	HepG2	liver:	n/a	chr1:226411233-226411249
8	NFIC	chr1:226410779-226411288	HepG2	liver:	n/a	n/a
9	SP1	chr1:226410679-226411260	HepG2	liver:	n/a	chr1:226411139-226411148 chr1:226410754-226410764 chr1:226411241-226411253 chr1:226411241-226411253 chr1:226411243-226411252 chr1:226411242-226411251 chr1:226410817-226410826 chr1:226410695-226410704
10	HNF4G	chr1:226410762-226411678	HepG2	liver:	n/a	chr1:226410954-226410966 chr1:226410951-226410969 chr1:226410954-226410966
11	FOXA2	chr1:226410760-226411236	HepG2	liver:	n/a	n/a
12	FOXA1	chr1:226410729-226411179	HepG2	liver:	n/a	n/a
13	ZBTB7A	chr1:226410662-226410961	HepG2	liver:	n/a	n/a
14	MYC	chr1:226410934-226410955	HepG2	liver:	n/a	n/a
15	HNF4A	chr1:226410720-226411809	HepG2	liver:	n/a	chr1:226410954-226410966 chr1:226410951-226410969 chr1:226410954-226410966
16	FOXA1	chr1:226410618-226411426	HepG2	liver:	n/a	n/a
17	HDAC2	chr1:226410805-226411411	HepG2	liver:	n/a	n/a
18	YY1	chr1:226410868-226411945	HepG2	liver:	n/a	chr1:226411079-226411090 chr1:226411233-226411247 chr1:226411059-226411073
19	RXRA	chr1:226410805-226411316	HepG2	liver:	n/a	n/a
20	CEBPD	chr1:226410801-226411448	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:226410847-226411832	HepG2	liver:	n/a	n/a
22	HNF4A	chr1:226410766-226411359	HepG2	liver:	n/a	chr1:226410954-226410966 chr1:226410951-226410969 chr1:226410954-226410966
23	FOXA1	chr1:226410717-226411125	HepG2	liver:	n/a	n/a
24	CEBPB	chr1:226410732-226411150	HepG2	liver:	n/a	n/a
25	MYBL2	chr1:226410756-226411284	HepG2	liver:	n/a	n/a
26	MAX	chr1:226410747-226412033	HepG2	liver:	n/a	n/a
27	RXRA	chr1:226410652-226411344	HepG2	liver:	n/a	n/a
28	HEY1	chr1:226410797-226411996	HepG2	liver:	n/a	chr1:226411236-226411251 chr1:226411132-226411147
29	POLR2A	chr1:226410856-226411970	HepG2	liver:	n/a	n/a
30	EP300	chr1:226410827-226411415	HepG2	liver:	n/a	n/a
31	SRF	chr1:226410772-226411100	H1-hESC	embryonic stem cell:	n/a	chr1:226410972-226410990 chr1:226410974-226410987 chr1:226410975-226410992 chr1:226410972-226410986 chr1:226410976-226410990 chr1:226410970-226410988
32	EP300	chr1:226410615-226411476	HepG2	liver:	n/a	n/a
33	TBP	chr1:226410862-226411514	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:226410916-226411896	HepG2	liver:	n/a	n/a
35	FOXA1	chr1:226410749-226411160	HepG2	liver:	n/a	n/a
36	MAZ	chr1:226410846-226411661	HepG2	liver:	n/a	n/a
37	ZBTB7A	chr1:226410694-226411343	HepG2	liver:	n/a	n/a
38	MXI1	chr1:226410804-226411945	HepG2	liver:	n/a	n/a
39	HNF4A	chr1:226410730-226411365	HepG2	liver:	n/a	chr1:226410954-226410966 chr1:226410951-226410969 chr1:226410954-226410966
40	TEAD4	chr1:226410619-226411158	HepG2	liver:	n/a	chr1:226410780-226410789
41	HNF4G	chr1:226410719-226411304	HepG2	liver:	n/a	chr1:226410954-226410966 chr1:226410951-226410969 chr1:226410954-226410966
42	HDAC2	chr1:226410755-226411784	HepG2	liver:	n/a	n/a
43	SRF	chr1:226410793-226411133	HepG2	liver:	n/a	chr1:226410972-226410990 chr1:226410974-226410987 chr1:226410975-226410992 chr1:226410972-226410986 chr1:226410976-226410990 chr1:226410970-226410988

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226401377..226404931-chr1:226406831..226410956,4	MCF-7	breast:

Variant related genes	Relation type
MIXL1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10127753	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10127776	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10127970	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10799341	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799343	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10799344	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10799346	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799347	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10915962	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915964	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10915970	0.85[EUR][1000 genomes]
rs1219658	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1417766	0.85[EUR][1000 genomes]
rs1813323	0.95[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs2126573	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2126577	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2126578	0.84[EUR][1000 genomes]
rs2169567	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2254723	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2377026	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2377028	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2377029	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2615799	1.00[CEU][hapmap];0.81[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2615803	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2666429	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2889537	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2927338	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4418563	0.81[ASN][1000 genomes]
rs4612598	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6605032	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7552015	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9725097	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3425958	chr1:226410154-226412702	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10753416	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226375200-226411000	Weak transcription	Right Atrium	heart
2	chr1:226399000-226411200	Weak transcription	Gastric	stomach
3	chr1:226408600-226411000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:226408800-226411600	Weak transcription	K562	blood
5	chr1:226409000-226411000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:226410600-226411000	Flanking Active TSS	HepG2	liver
7	chr1:226410600-226411200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:226410600-226412200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:226410600-226412400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:226410600-226412800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:226410800-226411000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr1:226410800-226411000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:226410800-226411000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:226410800-226411000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:226410800-226411000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr1:226410800-226411000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr1:226410800-226411000	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
18	chr1:226410800-226411000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:226410800-226411000	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr1:226410800-226411000	Enhancers	Right Ventricle	heart
21	chr1:226410800-226411200	Active TSS	Primary hematopoietic stem cells	blood
22	chr1:226410800-226411200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
23	chr1:226410800-226411200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:226410800-226411200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:226410800-226411200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:226410800-226411200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
27	chr1:226410800-226411200	Bivalent Enhancer	Placenta	Placenta
28	chr1:226410800-226411200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
29	chr1:226410800-226411200	Enhancers	GM12878-XiMat	blood
30	chr1:226410800-226411400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr1:226410800-226411600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:226410800-226411600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
33	chr1:226410800-226411800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:226410800-226411800	Enhancers	Fetal Heart	heart
35	chr1:226410800-226412000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:226410800-226412000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
37	chr1:226410800-226412000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:226410800-226412200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr1:226410800-226412200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:226410800-226412400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:226410800-226412400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr1:226410800-226412400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:226410800-226412400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
44	chr1:226410800-226412800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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