Variant report

Variant	rs2053769
Chromosome Location	chr4:87908007-87908008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87907221..87909869-chr4:87913541..87915799,2	K562	blood:
2	chr4:87906047..87909235-chr4:87925490..87928515,3	K562	blood:
3	chr4:87906409..87908323-chr4:87926209..87928101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10015639	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10032244	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs11729622	0.94[ASN][1000 genomes]
rs12651081	0.85[LWK][hapmap]
rs13126334	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127250	0.96[ASN][1000 genomes]
rs1447994	0.81[ASN][1000 genomes]
rs2007132	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2053770	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28495007	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3113494	0.81[LWK][hapmap]
rs340626	0.85[ASN][1000 genomes]
rs340630	0.84[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs340633	0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs340636	0.84[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs340637	0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs340638	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs340639	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.91[ASN][1000 genomes]
rs340641	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs340642	0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs340643	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs340648	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340650	0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs340651	0.87[ASN][1000 genomes]
rs375795	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs388401	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4274814	0.85[LWK][hapmap]
rs4386567	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs443459	0.85[ASN][1000 genomes]
rs4536898	0.85[LWK][hapmap]
rs4693796	0.86[ASN][1000 genomes]
rs4693798	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693800	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58633957	0.85[ASN][1000 genomes]
rs6531941	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6531946	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6531948	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811587	0.93[ASN][1000 genomes]
rs6839933	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs867196	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9715807	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2053769	AFF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:87892800-87909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:87894400-87911000	Weak transcription	Pancreas	Pancrea
7	chr4:87894600-87915600	Weak transcription	Lung	lung
8	chr4:87894600-87921000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:87895200-87909400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:87895400-87920000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:87896200-87916000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:87896200-87919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:87896800-87918800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:87897600-87915600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:87898200-87915400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:87899000-87915400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:87899000-87915400	Weak transcription	Left Ventricle	heart
18	chr4:87899000-87920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:87899000-87921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:87899200-87911000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:87899200-87913200	Weak transcription	Liver	Liver
22	chr4:87899200-87920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:87899200-87922800	Weak transcription	Osteobl	bone
24	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
25	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:87900000-87915600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:87900000-87924400	Weak transcription	NHEK	skin
28	chr4:87900200-87908200	Weak transcription	Stomach Mucosa	stomach
29	chr4:87900200-87920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:87901000-87913000	Weak transcription	Fetal Intestine Large	intestine
31	chr4:87901200-87913200	Weak transcription	HepG2	liver
32	chr4:87903200-87918800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:87903400-87908400	Weak transcription	GM12878-XiMat	blood
35	chr4:87903400-87909600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:87903400-87915400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:87903600-87911400	Weak transcription	K562	blood
38	chr4:87903600-87915400	Weak transcription	Thymus	Thymus
39	chr4:87903600-87915400	Weak transcription	Dnd41	blood
40	chr4:87903600-87919800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:87903600-87921000	Weak transcription	Primary T cells from cord blood	blood
42	chr4:87903800-87913000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:87903800-87915600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:87903800-87919800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:87903800-87920000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:87904000-87915200	Weak transcription	Fetal Thymus	thymus
47	chr4:87904200-87909400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:87904400-87909400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:87904400-87909400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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