Variant report

Variant	rs3775228
Chromosome Location	chr4:87985166-87985167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87980531..87986351-chr4:87988282..87991075,4	K562	blood:
2	chr4:87855923..87858787-chr4:87983318..87985582,3	MCF-7	breast:
3	chr4:87856190..87858649-chr4:87983970..87987871,3	MCF-7	breast:
4	chr4:87927969..87930713-chr4:87984972..87986683,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10018904	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10023056	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10029915	0.86[CHB][hapmap]
rs10032710	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs13120301	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151450	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs151451	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17012334	0.81[CHB][hapmap]
rs17605615	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17668131	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1842685	0.81[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs2035403	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280952	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280954	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236676	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs236679	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236681	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733377	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3736668	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3755980	0.86[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs3755983	0.84[CHB][hapmap]
rs3755985	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3775226	0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs60695258	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3775228	AFF1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
2	chr4:87968800-87995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:87969000-87994600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:87970200-87989800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:87975000-87987800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:87976200-87989800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:87977000-87989400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:87979600-87990000	Weak transcription	Aorta	Aorta
9	chr4:87979800-87989600	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:87979800-87991800	Weak transcription	A549	lung
11	chr4:87980000-87990000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:87980000-87994000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:87980200-87989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:87980400-87988800	Weak transcription	Fetal Kidney	kidney
15	chr4:87980400-87989400	Weak transcription	Fetal Lung	lung
16	chr4:87980400-87989600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:87980600-87987400	Weak transcription	Lung	lung
18	chr4:87980600-87988400	Weak transcription	Brain Anterior Caudate	brain
19	chr4:87980600-87989800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:87980800-87988000	Weak transcription	Fetal Heart	heart
21	chr4:87980800-87991000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:87981000-87988200	Weak transcription	Adipose Nuclei	Adipose
23	chr4:87981000-87988600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:87981000-87989800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:87981000-87994600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:87981200-87987600	Weak transcription	Brain Substantia Nigra	brain
27	chr4:87981200-87988400	Weak transcription	Ovary	ovary
28	chr4:87981200-87988600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:87981200-87989600	Weak transcription	Brain Angular Gyrus	brain
30	chr4:87981200-87989600	Weak transcription	Spleen	Spleen
31	chr4:87981200-87990000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:87981200-87994000	Weak transcription	HUVEC	blood vessel
33	chr4:87981200-87994200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:87981600-87988200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:87981600-87988400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:87981800-87989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:87982200-87985200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:87982600-87985800	Weak transcription	Left Ventricle	heart
39	chr4:87982600-87987800	Weak transcription	NHDF-Ad	bronchial
40	chr4:87982600-87989600	Weak transcription	Pancreas	Pancrea
41	chr4:87982600-87989600	Weak transcription	Right Atrium	heart
42	chr4:87982600-87989800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:87982600-87989800	Weak transcription	Esophagus	oesophagus
44	chr4:87982600-87989800	Weak transcription	Stomach Mucosa	stomach
45	chr4:87982600-87992600	Weak transcription	Small Intestine	intestine
46	chr4:87982600-87994000	Weak transcription	Primary T cells from cord blood	blood
47	chr4:87982600-87999600	Weak transcription	K562	blood
48	chr4:87982800-87986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:87982800-87987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:87982800-87988400	Weak transcription	NHLF	lung

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