Variant report

Variant	rs1219658
Chromosome Location	chr1:226408451-226408452
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	CTCF	chr1:226408445-226408532	A549	lung:	n/a	chr1:226408483-226408501
2	SIN3AK20	chr1:226408380-226408913	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:226408435-226408558	K562	blood:	n/a	chr1:226408483-226408501
4	GATA3	chr1:226408412-226408991	MCF-7	breast:	n/a	n/a
5	CTCF	chr1:226408433-226408587	MCF-7	breast:	n/a	chr1:226408483-226408501
6	CTCF	chr1:226408429-226408548	Hela-S3	cervix:	n/a	chr1:226408483-226408501
7	CTCF	chr1:226408405-226408581	H1-hESC	embryonic stem cell:	n/a	chr1:226408483-226408501
8	RAD21	chr1:226408343-226408574	H1-hESC	embryonic stem cell:	n/a	chr1:226408481-226408500
9	RAD21	chr1:226408325-226408573	HepG2	liver:	n/a	chr1:226408481-226408500
10	CTCF	chr1:226408422-226408574	HepG2	liver:	n/a	chr1:226408483-226408501
11	FOXA1	chr1:226408405-226408772	T-47D	breast:	n/a	chr1:226408679-226408694
12	RAD21	chr1:226408401-226408540	K562	blood:	n/a	chr1:226408481-226408500
13	CTCF	chr1:226408420-226408570	HepG2	liver:	n/a	chr1:226408483-226408501
14	RAD21	chr1:226408194-226408711	H1-hESC	embryonic stem cell:	n/a	chr1:226408481-226408500 chr1:226408245-226408264
15	GATA3	chr1:226408261-226408914	MCF-7	breast:	n/a	n/a
16	CTCF	chr1:226408445-226408557	MCF-7	breast:	n/a	chr1:226408483-226408501
17	ARID3A	chr1:226408412-226408651	HepG2	liver:	n/a	n/a
18	CTCF	chr1:226408343-226408618	H1-hESC	embryonic stem cell:	n/a	chr1:226408483-226408501
19	CTCF	chr1:226408253-226408581	K562	blood:	n/a	chr1:226408483-226408501
20	CTCF	chr1:226408425-226408572	MCF-7	breast:	n/a	chr1:226408483-226408501
21	CTCF	chr1:226408400-226408550	K562	blood:	n/a	chr1:226408483-226408501
22	RAD21	chr1:226408388-226408665	HepG2	liver:	n/a	chr1:226408481-226408500
23	CTCF	chr1:226408409-226408573	MCF-7	breast:	n/a	chr1:226408483-226408501
24	CTCF	chr1:226408318-226408540	K562	blood:	n/a	chr1:226408483-226408501
25	CTCF	chr1:226408361-226408650	K562	blood:	n/a	chr1:226408483-226408501
26	CTCF	chr1:226408384-226408555	HepG2	liver:	n/a	chr1:226408483-226408501

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: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10127753	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10127776	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10127970	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10753416	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10799341	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799343	0.84[EUR][1000 genomes]
rs10799344	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799345	0.86[JPT][hapmap]
rs10799346	0.85[EUR][1000 genomes]
rs10799347	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10915962	0.91[EUR][1000 genomes]
rs10915964	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10915970	0.83[EUR][1000 genomes]
rs1417766	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1813323	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2126573	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2126577	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2126578	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2169567	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2254723	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2377026	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2377028	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2377029	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2615799	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2615803	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2666429	0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs2889537	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2927338	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4612598	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6605032	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552015	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9725097	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1219658	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 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	chr1:226401000-226410800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:226403400-226410800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:226403600-226410800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:226407600-226408600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:226407600-226408600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:226407600-226408800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:226407600-226408800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:226407600-226408800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:226407600-226408800	Enhancers	K562	blood
12	chr1:226407800-226408800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:226407800-226408800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:226407800-226408800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr1:226407800-226408800	Flanking Active TSS	HepG2	liver
16	chr1:226407800-226409000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:226408000-226408600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:226408000-226408600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:226408000-226409000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:226408000-226409200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:226408200-226408600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:226408400-226408600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:226408400-226408600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:226408400-226408800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links