Variant report

Variant	rs12139175
Chromosome Location	chr1:159902786-159902787
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	CTCF	chr1:159902660-159902810	GM12878	blood:	n/a	n/a
2	MYC	chr1:159902778-159902884	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr1:159902598-159903043	GM12878	blood:	n/a	n/a
4	NFIC	chr1:159902428-159902975	ECC-1	luminal epithelium:	n/a	n/a
5	MYC	chr1:159902784-159902984	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:159902754-159902996	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:159902749-159903038	MCF10A-Er-Src	breast:	n/a	n/a
8	NFIC	chr1:159902418-159902980	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr1:159902740-159902890	HMEC	breast:	n/a	n/a
10	FOS	chr1:159902729-159903086	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:159902754-159902995	MCF10A-Er-Src	breast:	n/a	n/a
12	NR3C1	chr1:159902626-159902832	ECC-1	luminal epithelium:	n/a	n/a
13	BHLHE40	chr1:159902774-159902974	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159899215..159903293-chr1:159903611..159908278,6	MCF-7	breast:

Variant related genes	Relation type
IGSF9	TF binding region
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10752634	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10797054	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10797055	0.86[ASN][1000 genomes]
rs10908750	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1320566	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1934074	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1934075	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6658042	0.89[ASN][1000 genomes]
rs6703466	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7524321	0.91[ASN][1000 genomes]
rs7526647	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv548054	chr1:159895979-159907441	Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159895800-159906600	Weak transcription	Small Intestine	intestine
2	chr1:159896000-159906000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:159896200-159906000	Genic enhancers	Fetal Intestine Small	intestine
4	chr1:159896400-159906000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:159896400-159906000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:159896400-159906600	Weak transcription	Right Atrium	heart
7	chr1:159896600-159906000	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr1:159896600-159906000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:159896600-159907200	Weak transcription	Fetal Heart	heart
10	chr1:159896600-159908600	Weak transcription	Fetal Kidney	kidney
11	chr1:159897000-159906200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:159897000-159906200	Strong transcription	Fetal Brain Female	brain
13	chr1:159897400-159905400	Strong transcription	Liver	Liver
14	chr1:159897800-159906400	Weak transcription	Fetal Brain Male	brain
15	chr1:159898000-159906000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:159898000-159906000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:159898200-159905800	Weak transcription	A549	lung
18	chr1:159899200-159906000	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr1:159899400-159906200	Weak transcription	Gastric	stomach
20	chr1:159899400-159906400	Strong transcription	Fetal Stomach	stomach
21	chr1:159899800-159905400	Weak transcription	Stomach Mucosa	stomach
22	chr1:159899800-159905800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:159899800-159906000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:159900000-159906400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:159900200-159902800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:159900200-159906000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:159900600-159905600	Strong transcription	Fetal Intestine Large	intestine
28	chr1:159900800-159905800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:159901200-159904400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:159901400-159903400	Weak transcription	Fetal Thymus	thymus
31	chr1:159901400-159903800	Enhancers	Esophagus	oesophagus
32	chr1:159901600-159904000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:159901600-159904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:159901600-159905000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:159901800-159903000	Enhancers	NHEK	skin
36	chr1:159901800-159904000	Enhancers	HMEC	breast
37	chr1:159902000-159903000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:159902000-159903000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:159902200-159902800	Enhancers	Lung	lung
40	chr1:159902200-159903000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:159902200-159903800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:159902200-159904400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:159902400-159902800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr1:159902400-159902800	Enhancers	Fetal Muscle Trunk	muscle
45	chr1:159902400-159903000	Enhancers	Spleen	Spleen
46	chr1:159902400-159903800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:159902400-159905200	Weak transcription	Brain Germinal Matrix	brain
48	chr1:159902600-159903000	Enhancers	Placenta	Placenta
49	chr1:159902600-159903000	Enhancers	GM12878-XiMat	blood
50	chr1:159902600-159903200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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