Variant report

Variant	rs946553
Chromosome Location	chr10:95512810-95512811
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	CEBPB	chr10:95512500-95512850	Hela-S3	cervix:	n/a	n/a
2	KAP1	chr10:95512557-95513027	HEK293	kidney:	n/a	n/a
3	FOS	chr10:95512551-95512866	MCF10A-Er-Src	breast:	n/a	chr10:95512705-95512716
4	FOS	chr10:95512549-95512898	MCF10A-Er-Src	breast:	n/a	chr10:95512705-95512716
5	JUND	chr10:95512460-95513179	HCT-116	colon:	n/a	n/a
6	RFX5	chr10:95512534-95512875	Hela-S3	cervix:	n/a	n/a
7	JUND	chr10:95512531-95512982	Hela-S3	cervix:	n/a	n/a
8	FOS	chr10:95512540-95512996	MCF10A-Er-Src	breast:	n/a	chr10:95512705-95512716
9	FOS	chr10:95512540-95512949	MCF10A-Er-Src	breast:	n/a	chr10:95512705-95512716
10	FOS	chr10:95512579-95512847	HUVEC	blood vessel:	n/a	chr10:95512705-95512716
11	CEBPB	chr10:95512609-95513011	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:95499932..95502310-chr10:95511778..95514024,2	MCF-7	breast:
2	chr10:95510815..95514212-chr10:95521474..95524274,4	MCF-7	breast:

Variant related genes	Relation type
LGI1	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10736078	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10786136	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882326	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919484	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4919491	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7913442	0.82[MKK][hapmap]
rs873920	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913047	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3346948	chr10:95421957-95532625	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs946553	HECTD2	cis	cerebellum	SCAN
rs946553	CEP55	cis	parietal	SCAN
rs946553	FRA10AC1	cis	parietal	SCAN
rs946553	C10orf4	Cis_1M	lymphoblastoid	RTeQTL
rs946553	FRA10AC1	cis	Artery Tibial	GTEx
rs946553	FRA10AC1	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95505800-95517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:95508200-95515000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:95509200-95514600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:95509600-95514800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:95509800-95514000	Weak transcription	Small Intestine	intestine
6	chr10:95510200-95517600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr10:95510800-95513200	Enhancers	Hela-S3	cervix
8	chr10:95510800-95514400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:95511000-95516800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr10:95511000-95517600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:95511600-95513800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:95511600-95517600	Enhancers	Fetal Stomach	stomach
13	chr10:95511800-95513000	Enhancers	NH-A	brain
14	chr10:95511800-95513000	Enhancers	Osteobl	bone
15	chr10:95511800-95514200	Enhancers	Stomach Mucosa	stomach
16	chr10:95512000-95513000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:95512000-95513800	Weak transcription	Colonic Mucosa	Colon
18	chr10:95512000-95515200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:95512000-95516000	Enhancers	Rectal Smooth Muscle	rectum
20	chr10:95512000-95516200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr10:95512000-95516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr10:95512000-95516600	Weak transcription	Brain Hippocampus Middle	brain
23	chr10:95512000-95516800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr10:95512000-95516800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr10:95512000-95517000	Weak transcription	Fetal Brain Male	brain
26	chr10:95512000-95517200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:95512000-95517600	Weak transcription	Lung	lung
28	chr10:95512000-95517600	Weak transcription	Psoas Muscle	Psoas
29	chr10:95512000-95517800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr10:95512000-95522200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:95512200-95513000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
32	chr10:95512200-95513000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr10:95512200-95513400	Enhancers	A549	lung
34	chr10:95512200-95513600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:95512200-95514000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr10:95512200-95514600	Enhancers	Brain Anterior Caudate	brain
37	chr10:95512200-95516000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr10:95512200-95516600	Weak transcription	Brain Substantia Nigra	brain
39	chr10:95512200-95516600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr10:95512200-95517000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr10:95512200-95517600	Weak transcription	Liver	Liver
42	chr10:95512200-95517600	Enhancers	Colon Smooth Muscle	Colon
43	chr10:95512400-95513400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr10:95512400-95516000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr10:95512600-95513600	Weak transcription	Right Atrium	heart
46	chr10:95512600-95513800	Weak transcription	Esophagus	oesophagus
47	chr10:95512600-95515400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr10:95512600-95515400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr10:95512600-95516800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:95512600-95517000	Weak transcription	Fetal Brain Female	brain

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