Variant report

Variant	rs4853010
Chromosome Location	chr2:74361113-74361114
allele	C/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	POLR2A	chr2:74360817-74361421	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:74357697..74362841-chr2:74424131..74428670,5	K562	blood:
2	chr2:74347023..74350379-chr2:74357531..74361133,4	K562	blood:
3	chr2:74360981..74362934-chr2:74373468..74376245,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000217702	TF binding region
ENSG00000163170	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11675066	0.88[ASN][1000 genomes]
rs12478482	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12619982	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2122290	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2177707	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280642	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280643	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280644	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41285981	0.88[AFR][1000 genomes]
rs41285983	0.88[AFR][1000 genomes]
rs4563249	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4852329	0.87[ASN][1000 genomes]
rs4853011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853012	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6731793	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72915068	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72915085	0.88[AFR][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	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv525117	chr2:74358901-74374641	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4853010	MGC10955	cis	Esophagus Mucosa	GTEx
rs4853010	FNBP1P1	cis	Esophagus Muscularis	GTEx
rs4853010	MGC10955	cis	Artery Tibial	GTEx
rs4853010	FNBP1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs4853010	MGC10955	cis	Esophagus Muscularis	GTEx
rs4853010	MGC10955	cis	Skin Sun Exposed Lower leg	GTEx
rs4853010	MGC10955	cis	lung	GTEx
rs4853010	FNBP1P1	cis	Artery Tibial	GTEx
rs4853010	MGC10955	cis	Thyroid	GTEx
rs4853010	MGC10955	cis	Artery Aorta	GTEx
rs4853010	MGC10955	cis	Adipose Subcutaneous	GTEx
rs4853010	FNBP1P1	cis	Artery Aorta	GTEx
rs4853010	MGC10955	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74348200-74367600	Weak transcription	Brain Anterior Caudate	brain
2	chr2:74348600-74361800	Weak transcription	Hela-S3	cervix
3	chr2:74354400-74373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:74355200-74373800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:74356400-74361400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:74357200-74361200	Weak transcription	NHLF	lung
7	chr2:74357600-74361200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:74357600-74361200	Weak transcription	Fetal Thymus	thymus
9	chr2:74357600-74361800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:74357600-74361800	Weak transcription	Right Ventricle	heart
11	chr2:74357600-74373800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:74357800-74361200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:74357800-74361400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:74357800-74361800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:74357800-74367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:74357800-74373600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:74358000-74361200	Weak transcription	HMEC	breast
18	chr2:74358000-74361600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:74358200-74361600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:74358200-74364800	Weak transcription	Esophagus	oesophagus
21	chr2:74358200-74373800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:74358400-74361200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:74358600-74367800	Weak transcription	Osteobl	bone
24	chr2:74358600-74368800	Weak transcription	NHDF-Ad	bronchial
25	chr2:74358800-74361200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:74358800-74361600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:74358800-74362000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:74358800-74373800	Weak transcription	HUVEC	blood vessel
29	chr2:74359000-74361200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:74359200-74361600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:74359200-74361800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:74359200-74373600	Weak transcription	Fetal Heart	heart
33	chr2:74359400-74361600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:74359400-74362400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:74359400-74362600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:74359400-74367600	Weak transcription	HSMM	muscle
37	chr2:74359400-74373600	Weak transcription	Primary B cells from cord blood	blood
38	chr2:74359600-74361200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:74359600-74361400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:74359600-74361400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:74359600-74361400	Weak transcription	GM12878-XiMat	blood
42	chr2:74359600-74361600	Weak transcription	Fetal Intestine Large	intestine
43	chr2:74359600-74373400	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:74359600-74373800	Weak transcription	Small Intestine	intestine
45	chr2:74359800-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:74359800-74373600	Weak transcription	NH-A	brain
47	chr2:74360000-74369800	Weak transcription	Colonic Mucosa	Colon
48	chr2:74360200-74361200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:74360200-74373600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:74360400-74361400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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