Variant report

Variant	rs10040400
Chromosome Location	chr5:112442386-112442387
allele	A/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	chr5:112426233-112442949	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr5:112440714-112442423	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112433359..112435186-chr5:112441396..112444395,2	K562	blood:
2	chr5:112428215..112429903-chr5:112440936..112443304,2	MCF-7	breast:

Variant related genes	Relation type
MCC	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10067901	0.88[ASN][1000 genomes]
rs10478110	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11241191	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11241192	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11241193	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11743369	0.89[ASN][1000 genomes]
rs11953203	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12187718	0.93[EUR][1000 genomes]
rs12187866	0.93[EUR][1000 genomes]
rs12188482	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12517185	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12517187	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12523053	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13156718	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13174483	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13179421	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13183472	0.93[EUR][1000 genomes]
rs13183638	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13184187	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36041392	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3884576	0.84[ASN][1000 genomes]
rs3922563	0.82[ASN][1000 genomes]
rs3922583	0.83[ASN][1000 genomes]
rs4078253	0.81[ASN][1000 genomes]
rs4078254	0.81[ASN][1000 genomes]
rs4235793	0.80[ASN][1000 genomes]
rs4262097	0.81[ASN][1000 genomes]
rs4705542	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705543	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705545	0.80[ASN][1000 genomes]
rs4705778	0.93[EUR][1000 genomes]
rs4705779	0.93[EUR][1000 genomes]
rs4705783	0.84[ASN][1000 genomes]
rs4705787	0.80[ASN][1000 genomes]
rs4705788	0.80[ASN][1000 genomes]
rs62374710	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6594682	0.86[EUR][1000 genomes]
rs6869399	0.89[ASN][1000 genomes]
rs7700271	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7704382	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7707142	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7731180	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326877	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9326878	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9326879	0.86[EUR][1000 genomes]
rs9885385	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:112426200-112445000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
8	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
10	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
11	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:112427600-112443200	Weak transcription	Brain Substantia Nigra	brain
13	chr5:112428600-112445000	Weak transcription	Placenta	Placenta
14	chr5:112431000-112442600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:112432200-112443200	Weak transcription	Lung	lung
17	chr5:112432200-112450200	Weak transcription	Spleen	Spleen
18	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
19	chr5:112433800-112443800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:112436000-112442400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:112437600-112445800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:112438000-112444400	Weak transcription	HMEC	breast
25	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
26	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
27	chr5:112438200-112444800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:112438200-112450000	Weak transcription	Adipose Nuclei	Adipose
29	chr5:112438200-112450200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:112438200-112452800	Weak transcription	Brain Anterior Caudate	brain
31	chr5:112438400-112443000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:112438400-112443000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:112439600-112454600	Weak transcription	Esophagus	oesophagus
34	chr5:112439800-112452600	Weak transcription	Fetal Lung	lung
35	chr5:112440000-112443400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:112440000-112445600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:112440000-112450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:112440200-112442400	Weak transcription	Liver	Liver
39	chr5:112440200-112445800	Weak transcription	Ovary	ovary
40	chr5:112440200-112446600	Weak transcription	Right Ventricle	heart
41	chr5:112440200-112447800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:112440200-112447800	Weak transcription	Right Atrium	heart
43	chr5:112440200-112448000	Weak transcription	Fetal Muscle Leg	muscle
44	chr5:112440200-112450000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:112440200-112450000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:112440200-112450000	Weak transcription	Fetal Stomach	stomach
47	chr5:112440200-112454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:112440400-112445800	Weak transcription	Fetal Heart	heart
49	chr5:112440600-112442600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:112441000-112444400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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