Variant report

Variant	rs2452601
Chromosome Location	chr4:95497654-95497655
allele	A/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	NFIC	chr4:95497339-95497827	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95496466..95498455-chr4:95499358..95501705,2	K562	blood:

Variant related genes	Relation type
PDLIM5	TF binding region
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10019142	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10019505	0.81[ASN][1000 genomes]
rs10033326	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs10034824	0.87[CHB][hapmap]
rs11724023	0.88[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11725850	0.80[EUR][1000 genomes]
rs11732687	0.88[CEU][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs12500426	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs12639623	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap]
rs12639887	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12639980	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12642449	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12645971	0.82[CHB][hapmap]
rs12649976	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13110115	0.82[CHB][hapmap]
rs13122786	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13135257	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13143502	0.85[CHB][hapmap]
rs17394213	0.82[ASN][1000 genomes]
rs2047025	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2172448	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2201092	0.82[EUR][1000 genomes]
rs2452010	0.82[CHB][hapmap]
rs2452574	0.82[CHB][hapmap]
rs2452575	0.82[CHB][hapmap]
rs2452580	0.86[CHB][hapmap]
rs2510768	0.82[ASN][1000 genomes]
rs2510769	0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2510772	0.82[CHB][hapmap]
rs2510781	0.82[CHB][hapmap]
rs28740868	0.89[EUR][1000 genomes]
rs3805263	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805264	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805266	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs3843444	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4634230	0.81[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs4699505	0.81[CHB][hapmap]
rs5013417	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60063444	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532491	0.81[ASN][1000 genomes]
rs6854173	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs7662466	0.81[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.88[MEX][hapmap]
rs7697149	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs902981	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs973995	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2452601	ATOH1	cis	cerebellum	SCAN
rs2452601	PDLIM5	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95483400-95524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:95484000-95507400	Weak transcription	Hela-S3	cervix
3	chr4:95489000-95507400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr4:95489200-95506800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:95489200-95507400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:95489200-95509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:95489400-95506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:95489600-95508200	Weak transcription	GM12878-XiMat	blood
9	chr4:95489600-95522800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:95489600-95539200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:95492000-95502200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:95493000-95498400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:95493200-95540200	Weak transcription	Small Intestine	intestine
14	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
15	chr4:95494000-95497800	Genic enhancers	Osteobl	bone
16	chr4:95494000-95506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:95495200-95506800	Weak transcription	Fetal Stomach	stomach
18	chr4:95495800-95498200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:95496000-95501800	Weak transcription	Fetal Lung	lung
20	chr4:95496200-95498600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
21	chr4:95496400-95498000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:95496600-95497800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:95496600-95497800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:95496600-95497800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr4:95496600-95497800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:95496600-95497800	Genic enhancers	NH-A	brain
27	chr4:95496600-95498000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:95496600-95498000	Strong transcription	HSMMtube	muscle
29	chr4:95496600-95498000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr4:95496600-95498200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:95496800-95497800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr4:95496800-95497800	Strong transcription	Primary hematopoietic stem cells	blood
33	chr4:95496800-95497800	Genic enhancers	Muscle Satellite Cultured Cells	--
34	chr4:95496800-95497800	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr4:95496800-95497800	Strong transcription	Fetal Intestine Large	intestine
36	chr4:95496800-95498000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr4:95496800-95498000	Strong transcription	NHEK	skin
38	chr4:95496800-95498200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:95496800-95498200	Strong transcription	HSMM	muscle
40	chr4:95496800-95499800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:95497000-95497800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:95497000-95498000	Strong transcription	HMEC	breast
43	chr4:95497000-95498400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:95497000-95498600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr4:95497000-95499800	Enhancers	Colon Smooth Muscle	Colon
46	chr4:95497200-95498200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:95497200-95498200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:95497200-95498200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:95497200-95498200	Weak transcription	Fetal Brain Female	brain
50	chr4:95497200-95498200	Weak transcription	NHDF-Ad	bronchial

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