Variant report

Variant	rs388401
Chromosome Location	chr4:87974415-87974416
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87925282..87929320-chr4:87973735..87976929,7	K562	blood:
2	chr4:87926523..87929308-chr4:87972685..87974681,2	MCF-7	breast:
3	chr4:87973947..87977443-chr4:87977698..87982276,5	K562	blood:
4	chr4:87925846..87930633-chr4:87974014..87981325,14	K562	blood:
5	chr4:87973183..87975185-chr4:87980947..87982650,2	MCF-7	breast:
6	chr4:87856023..87858203-chr4:87973033..87975111,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10015639	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10032244	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11729622	0.87[ASN][1000 genomes]
rs13126334	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13127250	0.88[ASN][1000 genomes]
rs1471251	0.82[CEU][hapmap]
rs2007132	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053769	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]
rs2053770	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28495007	0.81[EUR][1000 genomes]
rs340626	0.99[ASN][1000 genomes]
rs340630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340633	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs340636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs340637	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs340638	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs340639	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs340641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs340642	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340643	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340648	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340650	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs340651	0.86[ASN][1000 genomes]
rs375795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443459	0.99[ASN][1000 genomes]
rs4693798	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4693800	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58633957	0.99[ASN][1000 genomes]
rs6531941	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs6531946	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811587	0.90[ASN][1000 genomes]
rs6839933	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs867196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9715807	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
rs388401	AFF1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87960400-87975400	Weak transcription	Brain Germinal Matrix	brain
2	chr4:87961000-87979200	Weak transcription	HSMMtube	muscle
3	chr4:87963200-87982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
5	chr4:87964800-87979200	Weak transcription	A549	lung
6	chr4:87966200-87979200	Weak transcription	NH-A	brain
7	chr4:87967000-87975000	Strong transcription	Dnd41	blood
8	chr4:87967600-87975000	Weak transcription	Stomach Mucosa	stomach
9	chr4:87967800-87974600	Strong transcription	Fetal Intestine Large	intestine
10	chr4:87968600-87975400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:87968600-87979000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:87968800-87975000	Weak transcription	Gastric	stomach
13	chr4:87968800-87975400	Weak transcription	Spleen	Spleen
14	chr4:87968800-87975600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:87968800-87975800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:87968800-87975800	Weak transcription	NHEK	skin
17	chr4:87968800-87975800	Weak transcription	NHLF	lung
18	chr4:87968800-87976200	Weak transcription	NHDF-Ad	bronchial
19	chr4:87968800-87977600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:87968800-87978800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr4:87968800-87979000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:87968800-87979200	Weak transcription	HMEC	breast
23	chr4:87968800-87979200	Weak transcription	HSMM	muscle
24	chr4:87968800-87979400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:87968800-87979400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:87968800-87980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:87968800-87982000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:87968800-87982200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr4:87968800-87983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:87968800-87995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:87969000-87975000	Weak transcription	Esophagus	oesophagus
32	chr4:87969000-87976000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:87969000-87994600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:87969200-87974800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:87969200-87974800	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:87969600-87974600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:87970000-87974800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:87970000-87976000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:87970200-87974800	Weak transcription	Fetal Lung	lung
40	chr4:87970200-87975000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:87970200-87975800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:87970200-87976600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:87970200-87979200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr4:87970200-87979800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:87970200-87989800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:87970400-87982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:87970600-87974600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:87970600-87974600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:87970800-87976800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr4:87970800-87977000	Enhancers	Psoas Muscle	Psoas

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