Variant report

Variant	rs3008192
Chromosome Location	chr1:226404457-226404458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226401377..226404931-chr1:226406831..226410956,4	MCF-7	breast:
2	chr1:226373756..226375724-chr1:226401681..226404608,2	K562	blood:
3	chr1:226403910..226406210-chr1:226410473..226412333,2	K562	blood:
4	chr1:226403447..226405521-chr1:226495731..226497298,2	K562	blood:
5	chr1:226398182..226400458-chr1:226404038..226407539,3	K562	blood:
6	chr1:226403012..226406009-chr1:226466558..226469360,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183814	Chromatin interaction
ENSG00000185155	Chromatin interaction
ENSG00000182827	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10753418	0.88[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs10799340	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12136759	0.91[MEX][hapmap]
rs1219652	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1219654	0.91[ASN][1000 genomes]
rs1219659	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]
rs1228409	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1361559	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1877155	0.83[MEX][hapmap]
rs2199501	0.81[AMR][1000 genomes]
rs2306119	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2306121	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2927339	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008189	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008190	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668540	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703375	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7367845	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7368170	0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap]
rs9286998	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs9286999	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs9629826	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9660924	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9728663	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9728665	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3008192	ACBD3	cis	normal skin	skin_eQTL
rs3008192	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs3008192	JMJD4	cis	parietal	SCAN
rs3008192	PARP1	cis	cerebellum	SCAN

Chromatin state (count:21 , 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	chr1:226402400-226405600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:226402400-226405600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:226403200-226404600	Enhancers	K562	blood
7	chr1:226403200-226404800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:226403400-226407800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:226403400-226408000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:226403400-226408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:226403400-226410800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:226403600-226410800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:226404000-226405000	Enhancers	HepG2	liver
14	chr1:226404000-226408000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:226404200-226405400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:226404200-226405400	Weak transcription	Stomach Mucosa	stomach
17	chr1:226404200-226407600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:226404200-226407800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:226404200-226407800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:226404200-226408000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:226404400-226407600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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