Variant report

Variant	rs1219659
Chromosome Location	chr1:226408271-226408272
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	RAD21	chr1:226408194-226408711	H1-hESC	embryonic stem cell:	n/a	chr1:226408481-226408500 chr1:226408245-226408264
2	GATA3	chr1:226408261-226408914	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:226408253-226408581	K562	blood:	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: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10753418	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1219652	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1219654	0.92[ASN][1000 genomes]
rs1228409	0.89[ASN][1000 genomes]
rs1361559	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2199501	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2306119	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2927339	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3008189	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3008190	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3008191	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3008192	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6668540	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6703375	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7367845	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7368170	0.95[CHB][hapmap]
rs9286999	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9629826	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9728663	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9728665	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1219659	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs1219659	ACBD3	cis	normal skin	skin_eQTL

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	chr1:226407800-226408400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr1:226407800-226408400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:226407800-226408800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:226407800-226408800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:226407800-226408800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:226407800-226408800	Flanking Active TSS	HepG2	liver
18	chr1:226407800-226409000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:226408000-226408600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:226408000-226408600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:226408000-226409000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:226408000-226409200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:226408200-226408400	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:226408200-226408600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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