Variant report

Variant	rs17378777
Chromosome Location	chr4:95399873-95399874
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:95392600..95395263-chr4:95399484..95402281,2	K562	blood:
2	chr4:95395769..95400285-chr4:95406149..95409946,5	K562	blood:
3	chr4:95372993..95375546-chr4:95399640..95402667,3	K562	blood:
4	chr4:95398573..95401933-chr4:95402630..95406147,4	K562	blood:
5	chr4:95391486..95396177-chr4:95398178..95402962,4	K562	blood:
6	chr4:95397926..95400285-chr4:95407452..95409108,2	K562	blood:
7	chr4:95399809..95401815-chr4:95403356..95405505,3	K562	blood:
8	chr4:95373234..95374778-chr4:95399640..95401902,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1820475	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2011525	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433323	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2433326	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433327	0.88[CEU][hapmap];0.82[MEX][hapmap]
rs2438140	0.82[MEX][hapmap]
rs2438146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2438147	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2438148	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452553	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2510762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2510763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510765	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2510777	0.80[MEX][hapmap]
rs2639793	0.86[YRI][hapmap]
rs28697067	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34570027	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3805301	0.87[YRI][hapmap]
rs6812165	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs774982	0.88[CEU][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs774984	0.82[MEX][hapmap]
rs9990678	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9990976	0.81[CEU][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
rs17378777	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95374200-95400000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
3	chr4:95375800-95401600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:95387400-95410000	Weak transcription	NHLF	lung
5	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:95389600-95406000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:95393800-95401600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:95393800-95405600	Weak transcription	HSMMtube	muscle
9	chr4:95394000-95405000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:95394200-95401400	Weak transcription	Brain Anterior Caudate	brain
11	chr4:95394200-95404800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:95394400-95400600	Weak transcription	Adipose Nuclei	Adipose
13	chr4:95394400-95405800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:95394400-95407000	Weak transcription	NH-A	brain
15	chr4:95394400-95407800	Weak transcription	Aorta	Aorta
16	chr4:95394400-95419200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:95394600-95406000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:95395000-95400600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:95395400-95405000	Weak transcription	HSMM	muscle
21	chr4:95396200-95400000	Weak transcription	Pancreas	Pancrea
22	chr4:95396600-95419000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:95396800-95410000	Weak transcription	Fetal Intestine Large	intestine
24	chr4:95397800-95400600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:95398000-95401400	Weak transcription	HepG2	liver
26	chr4:95398400-95401600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:95398400-95407600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:95398400-95408800	Weak transcription	Brain Substantia Nigra	brain
29	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
30	chr4:95398600-95400200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:95398600-95400200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:95398600-95400200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:95398600-95400200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:95398600-95400600	Weak transcription	HUVEC	blood vessel
35	chr4:95398600-95401000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:95398600-95401600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:95398600-95401600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:95398600-95403400	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:95398600-95405800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr4:95398800-95400200	Weak transcription	Osteobl	bone
41	chr4:95399000-95400200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:95399000-95400200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:95399000-95400400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:95399000-95400400	Strong transcription	Fetal Intestine Small	intestine
45	chr4:95399000-95400400	Weak transcription	Right Ventricle	heart
46	chr4:95399000-95400600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:95399000-95400600	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:95399000-95400800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:95399000-95400800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:95399000-95401000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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