Variant report

Variant	rs16872604
Chromosome Location	chr4:22398060-22398061
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	POLR2A	chr4:22397979-22398239	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:22396985-22398766	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:22398024-22398159	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GPR125	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12331257	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13434988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs61736467	1.00[ASN][1000 genomes]
rs61791977	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61791978	1.00[ASN][1000 genomes]
rs61791979	1.00[ASN][1000 genomes]
rs61791982	1.00[ASN][1000 genomes]
rs61791983	1.00[ASN][1000 genomes]
rs61791986	1.00[ASN][1000 genomes]
rs61796260	1.00[ASN][1000 genomes]
rs61796261	1.00[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	nsv817467	chr4:21602921-22422816	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv428756	chr4:22239826-22406106	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16872604	GPR125	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22368800-22418600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:22371600-22449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:22372000-22400400	Weak transcription	Gastric	stomach
4	chr4:22382600-22409600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:22383200-22438000	Weak transcription	Lung	lung
6	chr4:22383600-22404200	Weak transcription	Fetal Kidney	kidney
7	chr4:22383600-22442800	Weak transcription	A549	lung
8	chr4:22384200-22400400	Weak transcription	Ovary	ovary
9	chr4:22384200-22401000	Weak transcription	Small Intestine	intestine
10	chr4:22384200-22413000	Weak transcription	Fetal Heart	heart
11	chr4:22385400-22430400	Weak transcription	Psoas Muscle	Psoas
12	chr4:22386000-22446600	Weak transcription	Fetal Thymus	thymus
13	chr4:22388000-22399200	Weak transcription	Fetal Brain Female	brain
14	chr4:22388000-22411400	Weak transcription	NHDF-Ad	bronchial
15	chr4:22388000-22416600	Weak transcription	NHLF	lung
16	chr4:22388200-22432400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:22388200-22442800	Weak transcription	Brain Germinal Matrix	brain
18	chr4:22388400-22417800	Weak transcription	HUVEC	blood vessel
19	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
21	chr4:22389200-22402400	Weak transcription	Esophagus	oesophagus
22	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
23	chr4:22390200-22404800	Weak transcription	Pancreas	Pancrea
24	chr4:22390200-22414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:22390400-22398200	Weak transcription	Left Ventricle	heart
26	chr4:22390400-22399400	Weak transcription	Adipose Nuclei	Adipose
27	chr4:22390400-22400400	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:22390400-22402000	Weak transcription	Right Ventricle	heart
29	chr4:22390600-22399000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:22390600-22399000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:22390600-22399200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:22390600-22399600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:22390600-22400400	Weak transcription	Aorta	Aorta
34	chr4:22390600-22400400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:22390600-22404400	Weak transcription	Primary T cells from cord blood	blood
36	chr4:22390600-22407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:22390600-22423600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:22390600-22439600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:22390600-22456200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:22390800-22398800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:22390800-22399200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:22390800-22399200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:22390800-22399200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:22390800-22399400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:22390800-22399600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:22390800-22400400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:22390800-22407800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:22390800-22418000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:22390800-22420400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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