Variant report

Variant	rs1725604
Chromosome Location	chr7:101914135-101914136
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	EP300	chr7:101913049-101915087	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr7:101913065-101914878	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:101912928..101918938-chr7:101926951..101931541,5	K562	blood:
2	chr7:101456296..101461488-chr7:101913983..101918398,7	MCF-7	breast:
3	chr7:101905664..101912397-chr7:101912509..101916552,6	K562	blood:
4	chr7:101913664..101916452-chr7:101928530..101931361,3	MCF-7	breast:

Variant related genes	Relation type
CUX1	TF binding region
ENSG00000160999	Chromatin interaction
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1613236	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725603	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1734733	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1734735	0.86[ASN][1000 genomes]
rs712837	0.86[ASN][1000 genomes]
rs712838	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712839	0.84[ASN][1000 genomes]
rs712840	0.84[ASN][1000 genomes]
rs803063	0.87[ASN][1000 genomes]
rs803064	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs803065	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs803069	0.82[ASN][1000 genomes]
rs803082	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464662	chr7:101912320-101949128	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv464663	chr7:101912320-101949128	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv607996	chr7:101912320-101949128	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	24 gene(s)	inside rSNPs	diseases
4	nsv607997	chr7:101912320-101949128	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	24 gene(s)	inside rSNPs	diseases
5	esv2758126	chr7:101912320-102005026	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
6	esv2759548	chr7:101912320-102005026	Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
7	esv1814780	chr7:101912320-102375950	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	esv1819566	chr7:101912320-102375950	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Enhancers Genic enhancers 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
9	esv1822347	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	esv1825708	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
11	esv1842898	chr7:101912320-102375950	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	esv1847418	chr7:101912320-102375950	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
13	nsv427798	chr7:101912320-102375950	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
14	nsv428182	chr7:101912320-102375950	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
15	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
16	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
17	esv1822373	chr7:101913187-101969458	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1725604	SLC26A5	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101892800-101928000	Weak transcription	Esophagus	oesophagus
2	chr7:101892800-101928400	Weak transcription	Right Ventricle	heart
3	chr7:101894000-101916800	Weak transcription	Lung	lung
4	chr7:101897400-101915400	Weak transcription	Pancreas	Pancrea
5	chr7:101897600-101928000	Weak transcription	Primary T cells from cord blood	blood
6	chr7:101898000-101928200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:101898200-101922600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:101899800-101922800	Weak transcription	Right Atrium	heart
9	chr7:101900200-101915600	Weak transcription	Fetal Intestine Small	intestine
10	chr7:101902000-101917000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:101904600-101922800	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:101904600-101928200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:101905000-101915400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:101905200-101915400	Weak transcription	Brain Substantia Nigra	brain
15	chr7:101908000-101917400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:101908000-101929200	Weak transcription	Gastric	stomach
17	chr7:101908400-101922600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:101910200-101928400	Weak transcription	Liver	Liver
19	chr7:101912200-101915800	Weak transcription	K562	blood
20	chr7:101912200-101922600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:101912400-101922600	Weak transcription	Fetal Thymus	thymus
22	chr7:101913000-101914400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr7:101913000-101914400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:101913000-101914400	Enhancers	Fetal Muscle Leg	muscle
25	chr7:101913200-101914200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr7:101913200-101914200	Bivalent Enhancer	Fetal Stomach	stomach
27	chr7:101913400-101914400	Enhancers	Brain Cingulate Gyrus	brain
28	chr7:101913400-101914400	Enhancers	Brain Hippocampus Middle	brain
29	chr7:101913400-101916600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:101913600-101915200	Weak transcription	HepG2	liver
31	chr7:101913600-101915400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:101913800-101914400	Genic enhancers	Spleen	Spleen
33	chr7:101913800-101914600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:101913800-101915000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:101913800-101916000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr7:101914000-101914200	Enhancers	Fetal Brain Female	brain
37	chr7:101914000-101915400	Weak transcription	Fetal Lung	lung

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