Variant report

Variant	rs2452563
Chromosome Location	chr4:95424226-95424227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95407018..95410385-chr4:95421920..95424793,3	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1082513	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12645971	0.84[CEU][hapmap]
rs13110115	0.84[CEU][hapmap]
rs13143502	0.84[CEU][hapmap]
rs1493109	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1493111	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1845176	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433327	0.86[MEX][hapmap]
rs2438140	0.84[CHB][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2452010	0.92[CEU][hapmap];0.81[MEX][hapmap]
rs2452555	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2452567	0.98[ASN][1000 genomes]
rs2452571	0.80[CEU][hapmap]
rs2452574	0.92[CEU][hapmap]
rs2452575	0.83[CEU][hapmap]
rs2452580	0.80[CEU][hapmap]
rs2510769	0.81[CEU][hapmap]
rs2510777	0.81[CEU][hapmap]
rs2510781	0.92[CEU][hapmap];0.81[MEX][hapmap]
rs2510789	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2510793	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510796	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510797	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555215	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2639794	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792666	0.84[CEU][hapmap]
rs4699505	0.84[CEU][hapmap]
rs774984	0.85[CHB][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs774985	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774987	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774990	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774991	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9990976	0.82[MEX][hapmap]

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	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
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2452563	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
4	chr4:95400800-95440000	Weak transcription	Lung	lung
5	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:95407200-95428000	Weak transcription	Placenta	Placenta
7	chr4:95408000-95428000	Weak transcription	K562	blood
8	chr4:95411000-95427800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:95412400-95424600	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:95412800-95426000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:95412800-95428400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr4:95413000-95426200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:95413200-95427400	Weak transcription	A549	lung
14	chr4:95413200-95428000	Weak transcription	Hela-S3	cervix
15	chr4:95413400-95425800	Weak transcription	HSMMtube	muscle
16	chr4:95413400-95428000	Weak transcription	NH-A	brain
17	chr4:95413400-95428400	Weak transcription	NHLF	lung
18	chr4:95413600-95425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:95414600-95429000	Weak transcription	Esophagus	oesophagus
20	chr4:95415400-95425800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:95415400-95429000	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:95415400-95440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:95416200-95427400	Weak transcription	Fetal Intestine Large	intestine
24	chr4:95416400-95425600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:95417000-95427200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:95417200-95426800	Weak transcription	HUVEC	blood vessel
27	chr4:95417200-95428000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:95418000-95425800	Weak transcription	Right Ventricle	heart
29	chr4:95418000-95430800	Weak transcription	Pancreas	Pancrea
30	chr4:95419600-95428400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:95419800-95427800	Weak transcription	Aorta	Aorta
32	chr4:95419800-95428600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:95420000-95427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:95420000-95427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:95420000-95427800	Weak transcription	HMEC	breast
36	chr4:95420000-95427800	Weak transcription	NHEK	skin
37	chr4:95420000-95428000	Weak transcription	HSMM	muscle
38	chr4:95420200-95427600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:95421000-95425400	Enhancers	Fetal Heart	heart
40	chr4:95421200-95425400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:95421200-95426400	Weak transcription	Fetal Intestine Small	intestine
42	chr4:95421200-95429000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:95421200-95429600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:95421200-95440000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:95421400-95428600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:95421400-95431400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr4:95421600-95440000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:95422400-95426400	Weak transcription	Right Atrium	heart
49	chr4:95422400-95428400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:95422400-95429000	Weak transcription	Ovary	ovary

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