Variant report

Variant	rs2510772
Chromosome Location	chr4:95470815-95470816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95466562..95469843-chr4:95470075..95473924,5	K562	blood:
2	chr4:95464708..95469426-chr4:95470140..95474023,5	K562	blood:
3	chr4:95443271..95445067-chr4:95469458..95471347,2	K562	blood:
4	chr4:95386864..95390124-chr4:95470356..95473538,3	K562	blood:
5	chr4:95456523..95459012-chr4:95469903..95471763,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10019142	0.84[ASN][1000 genomes]
rs10033326	0.86[CHB][hapmap]
rs10034824	0.94[CHB][hapmap]
rs1032420	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12500426	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs12639623	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs12639887	0.82[CHB][hapmap]
rs12642449	0.82[CHB][hapmap]
rs12645971	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13110115	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13122786	0.82[CHB][hapmap]
rs13143502	0.84[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs13146878	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17021775	0.81[LWK][hapmap];0.81[YRI][hapmap]
rs17394213	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1972011	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452008	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452010	0.84[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs2452569	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2452570	0.86[ASN][1000 genomes]
rs2452571	0.88[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2452572	0.83[ASN][1000 genomes]
rs2452574	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs2452575	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs2452578	0.80[CHB][hapmap]
rs2452580	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452582	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452584	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452585	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452586	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452589	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2452601	0.82[CHB][hapmap]
rs2510768	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2510769	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2510774	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2510775	0.87[ASN][1000 genomes]
rs2510776	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510777	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510779	0.82[ASN][1000 genomes]
rs2510780	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2510781	0.84[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs28740868	0.88[ASN][1000 genomes]
rs3792666	0.84[CEU][hapmap];0.89[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3805263	0.85[CHB][hapmap]
rs3805266	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs3805285	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3843444	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4634230	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4699505	0.84[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6854173	0.86[CHB][hapmap]
rs7662466	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs902981	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2510772	ATOH1	cis	cerebellum	SCAN
rs2510772	PDLIM5	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:95457400-95485400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:95458000-95480400	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:95458200-95483000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:95458200-95488800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:95459000-95473000	Weak transcription	Fetal Kidney	kidney
7	chr4:95459000-95480400	Weak transcription	Adipose Nuclei	Adipose
8	chr4:95459600-95471000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:95459800-95481200	Weak transcription	Aorta	Aorta
10	chr4:95460200-95472400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:95463000-95480400	Weak transcription	Right Ventricle	heart
12	chr4:95463000-95487800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:95463200-95481200	Weak transcription	Left Ventricle	heart
14	chr4:95466000-95474800	Weak transcription	Psoas Muscle	Psoas
15	chr4:95466000-95475000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:95467000-95471800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:95467600-95479400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:95468400-95471000	Enhancers	Hela-S3	cervix
19	chr4:95468600-95471000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr4:95468800-95472600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:95469000-95472600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:95469600-95471000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:95469800-95471000	Enhancers	Stomach Mucosa	stomach
24	chr4:95469800-95476600	Enhancers	Fetal Heart	heart
25	chr4:95470000-95471000	Enhancers	Placenta	Placenta
26	chr4:95470000-95471000	Enhancers	HMEC	breast
27	chr4:95470000-95471200	Weak transcription	Primary T cells from cord blood	blood
28	chr4:95470000-95472600	Enhancers	HUVEC	blood vessel
29	chr4:95470000-95489200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:95470200-95471000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr4:95470200-95471000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
32	chr4:95470200-95471600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:95470400-95471000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:95470400-95471000	Genic enhancers	K562	blood
35	chr4:95470400-95472800	Weak transcription	NHDF-Ad	bronchial
36	chr4:95470400-95473000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:95470400-95473200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:95470400-95473200	Enhancers	HSMMtube	muscle
39	chr4:95470400-95477800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:95470400-95479600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:95470400-95479600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:95470400-95480400	Weak transcription	NHLF	lung
43	chr4:95470400-95482600	Weak transcription	HepG2	liver
44	chr4:95470400-95484800	Weak transcription	Fetal Intestine Large	intestine
45	chr4:95470600-95471200	Enhancers	A549	lung
46	chr4:95470600-95471400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:95470600-95471600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:95470600-95471600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:95470600-95472400	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:95470600-95472600	Weak transcription	Liver	Liver

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