Variant report

Variant	rs16872669
Chromosome Location	chr4:22457478-22457479
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	FOS	chr4:22457418-22457500	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr4:22457314-22457505	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
GPR125	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10805234	0.80[MKK][hapmap]
rs10938897	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11933055	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13102647	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13109695	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs13135121	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs13140185	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13140367	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1462995	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1462996	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs1462997	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes]
rs1564135	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs1841824	0.81[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs1841825	0.81[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs1841828	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs1947738	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4583743	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4611916	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4627850	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6448155	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6448156	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6823735	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71182940	0.87[ASN][1000 genomes]
rs7670841	0.81[MEX][hapmap];0.80[MKK][hapmap]
rs964549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16872669	LGI2	cis	cerebellum	SCAN
rs16872669	SLC34A2	cis	parietal	SCAN
rs16872669	GPR125	cis	cerebellum	SCAN

Chromatin state (count:89 , 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	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:22400800-22461800	Weak transcription	Gastric	stomach
7	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
9	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
10	chr4:22424400-22457800	Weak transcription	Dnd41	blood
11	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:22428600-22460600	Weak transcription	Placenta	Placenta
13	chr4:22429400-22457800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:22432400-22460400	Weak transcription	Small Intestine	intestine
15	chr4:22433800-22479200	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:22434000-22461200	Weak transcription	Brain Anterior Caudate	brain
17	chr4:22437400-22476400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:22437800-22459600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:22437800-22465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:22439200-22458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:22443400-22471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:22443400-22472400	Weak transcription	Ovary	ovary
23	chr4:22443400-22473600	Weak transcription	Fetal Brain Female	brain
24	chr4:22443600-22470800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:22443600-22476200	Weak transcription	A549	lung
26	chr4:22443800-22474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:22444000-22470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:22447200-22467600	Weak transcription	Thymus	Thymus
29	chr4:22447200-22473800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:22447200-22475000	Weak transcription	NHLF	lung
31	chr4:22447800-22473400	Weak transcription	Brain Germinal Matrix	brain
32	chr4:22448000-22461400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:22448600-22472600	Weak transcription	Primary T cells from cord blood	blood
34	chr4:22449600-22458200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:22450200-22457800	Weak transcription	Left Ventricle	heart
36	chr4:22450200-22459600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:22450200-22471000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:22450200-22473800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:22450200-22473800	Weak transcription	NH-A	brain
40	chr4:22450400-22460200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:22450400-22461800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:22450400-22474800	Weak transcription	Adipose Nuclei	Adipose
43	chr4:22450400-22476000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:22450400-22484000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:22450800-22464200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:22451200-22459600	Weak transcription	Liver	Liver
48	chr4:22451400-22464000	Weak transcription	Fetal Stomach	stomach
49	chr4:22453400-22458600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:22453400-22460800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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