Variant report

Variant	rs13109198
Chromosome Location	chr4:22460103-22460104
allele	G/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	chr4:22459657-22460306	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr4:22459713-22460206	ECC-1	luminal epithelium:	n/a	chr4:22459919-22459929
3	TCF12	chr4:22459767-22460250	ECC-1	luminal epithelium:	n/a	chr4:22459919-22459929

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22457536..22463707-chr4:22514115..22518559,7	MCF-7	breast:
2	chr4:22449726..22452368-chr4:22458347..22461364,3	MCF-7	breast:

Variant related genes	Relation type
GPR125	TF binding region
ENSG00000152990	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10003859	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10003883	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10014897	0.81[ASN][1000 genomes]
rs10516411	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13110697	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13129189	0.93[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs13139516	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13145061	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13152378	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16872664	0.86[ASN][1000 genomes]
rs16872682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2323523	1.00[YRI][hapmap]
rs28386903	0.81[ASN][1000 genomes]
rs28437151	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28726245	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs34228241	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35426712	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35852147	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35926750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36111920	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4697013	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4697298	1.00[YRI][hapmap]
rs4697300	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4697301	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4697304	0.89[ASN][1000 genomes]
rs4697306	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57133360	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59022936	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60379399	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61744997	0.87[EUR][1000 genomes]
rs71608917	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs716411	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
3	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
4	chr4:22400800-22461800	Weak transcription	Gastric	stomach
5	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
7	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
8	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:22428600-22460600	Weak transcription	Placenta	Placenta
10	chr4:22432400-22460400	Weak transcription	Small Intestine	intestine
11	chr4:22433800-22479200	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:22434000-22461200	Weak transcription	Brain Anterior Caudate	brain
13	chr4:22437400-22476400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:22437800-22465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:22443400-22471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:22443400-22472400	Weak transcription	Ovary	ovary
17	chr4:22443400-22473600	Weak transcription	Fetal Brain Female	brain
18	chr4:22443600-22470800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:22443600-22476200	Weak transcription	A549	lung
20	chr4:22443800-22474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:22444000-22470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:22447200-22467600	Weak transcription	Thymus	Thymus
23	chr4:22447200-22473800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:22447200-22475000	Weak transcription	NHLF	lung
25	chr4:22447800-22473400	Weak transcription	Brain Germinal Matrix	brain
26	chr4:22448000-22461400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:22448600-22472600	Weak transcription	Primary T cells from cord blood	blood
28	chr4:22450200-22471000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:22450200-22473800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr4:22450200-22473800	Weak transcription	NH-A	brain
31	chr4:22450400-22460200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:22450400-22461800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:22450400-22474800	Weak transcription	Adipose Nuclei	Adipose
34	chr4:22450400-22476000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:22450400-22484000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:22450800-22464200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:22451400-22464000	Weak transcription	Fetal Stomach	stomach
39	chr4:22453400-22460800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:22454400-22462200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:22455600-22474200	Weak transcription	Fetal Thymus	thymus
42	chr4:22456400-22461600	Weak transcription	HMEC	breast
43	chr4:22456400-22476200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:22456600-22462800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:22456600-22466200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:22456800-22460400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:22456800-22466200	Weak transcription	Right Ventricle	heart
48	chr4:22456800-22476000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:22456800-22479000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:22456800-22485000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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