Variant report

Variant	rs6703466
Chromosome Location	chr1:159908393-159908394
allele	A/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	RUNX3	chr1:159908098-159908437	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:159908305-159908432	MCF-7	breast:	n/a	n/a
3	BATF	chr1:159908178-159908487	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:159908383-159908435	H1-hESC	embryonic stem cell:	n/a	n/a
5	EBF1	chr1:159908114-159908502	GM12878	blood:	n/a	n/a
6	RUNX3	chr1:159908096-159908471	GM12878	blood:	n/a	n/a
7	IRF4	chr1:159908193-159908494	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159907235..159909524-chr1:159933511..159935771,2	MCF-7	breast:
2	chr1:159907782..159910427-chr1:159933319..159935593,2	MCF-7	breast:

Variant related genes	Relation type
IGSF9	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10752634	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10797054	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10797055	0.93[ASN][1000 genomes]
rs10908750	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12139175	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1320566	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1934075	0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs6658042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524321	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv464150	chr1:159860917-159908393	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv548052	chr1:159860917-159908393	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv548053	chr1:159885500-159908393	Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv516637	chr1:159889686-159908393	Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159896600-159908600	Weak transcription	Fetal Kidney	kidney
2	chr1:159905400-159908400	Enhancers	Primary B cells from cord blood	blood
3	chr1:159905400-159908600	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:159905400-159909600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:159905400-159909800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:159905600-159908400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:159905800-159908400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:159905800-159908600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:159905800-159908600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:159905800-159911400	Enhancers	Placenta	Placenta
11	chr1:159905800-159913600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:159906000-159908400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:159906000-159908600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:159906000-159908600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:159906000-159908600	Enhancers	Fetal Thymus	thymus
16	chr1:159906000-159909000	Enhancers	Liver	Liver
17	chr1:159906000-159909000	Enhancers	Esophagus	oesophagus
18	chr1:159906000-159909000	Enhancers	HMEC	breast
19	chr1:159906000-159909400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr1:159906000-159910600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:159906000-159911000	Weak transcription	Brain Germinal Matrix	brain
22	chr1:159906200-159908400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:159906200-159908600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:159906200-159908600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr1:159906400-159908600	Enhancers	Fetal Brain Female	brain
26	chr1:159906400-159909000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:159906400-159909600	Genic enhancers	NHEK	skin
28	chr1:159906600-159908600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:159906600-159909800	Enhancers	Small Intestine	intestine
30	chr1:159906800-159908400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:159906800-159910200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:159907000-159915200	Weak transcription	Gastric	stomach
33	chr1:159907200-159908400	Enhancers	Fetal Heart	heart
34	chr1:159907200-159908400	Flanking Active TSS	Stomach Mucosa	stomach
35	chr1:159907200-159908600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:159907400-159909600	Weak transcription	A549	lung
37	chr1:159907400-159910600	Weak transcription	Fetal Brain Male	brain
38	chr1:159907400-159911400	Weak transcription	Thymus	Thymus
39	chr1:159907600-159908800	Enhancers	GM12878-XiMat	blood
40	chr1:159907600-159909400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:159907600-159909600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:159907600-159909800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:159907600-159909800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:159907600-159909800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:159907600-159910000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:159907600-159910600	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:159907800-159908400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr1:159907800-159908600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr1:159907800-159910400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:159908000-159908400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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