Variant report

Variant	rs236681
Chromosome Location	chr4:87988508-87988509
allele	G/T
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	chr4:87980531..87984297-chr4:87985969..87990791,4	K562	blood:
3	chr4:87985538..87989484-chr4:87990047..87992954,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10018904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10023056	0.86[CHB][hapmap]
rs10029915	0.86[CHB][hapmap]
rs10032710	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs11097127	0.85[YRI][hapmap]
rs13120301	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151450	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs151451	0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs17012334	0.81[CHB][hapmap]
rs17605615	0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17668131	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1842685	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs2035403	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2280952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236676	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs236679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733377	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3736668	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3736669	0.81[YRI][hapmap]
rs3755980	0.86[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap]
rs3755983	0.83[CHB][hapmap]
rs3755985	0.85[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3775226	0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs3775228	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]
rs60695258	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[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
rs236681	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	chr4:87976200-87989800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:87977000-87989400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:87979600-87990000	Weak transcription	Aorta	Aorta
8	chr4:87979800-87989600	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:87979800-87991800	Weak transcription	A549	lung
10	chr4:87980000-87990000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:87980000-87994000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr4:87980200-87989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:87980400-87988800	Weak transcription	Fetal Kidney	kidney
14	chr4:87980400-87989400	Weak transcription	Fetal Lung	lung
15	chr4:87980400-87989600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:87980600-87989800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:87980800-87991000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr4:87981000-87988600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:87981000-87989800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:87981000-87994600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:87981200-87988600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:87981200-87989600	Weak transcription	Brain Angular Gyrus	brain
23	chr4:87981200-87989600	Weak transcription	Spleen	Spleen
24	chr4:87981200-87990000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:87981200-87994000	Weak transcription	HUVEC	blood vessel
26	chr4:87981200-87994200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:87981800-87989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:87982600-87989600	Weak transcription	Pancreas	Pancrea
29	chr4:87982600-87989600	Weak transcription	Right Atrium	heart
30	chr4:87982600-87989800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:87982600-87989800	Weak transcription	Esophagus	oesophagus
32	chr4:87982600-87989800	Weak transcription	Stomach Mucosa	stomach
33	chr4:87982600-87992600	Weak transcription	Small Intestine	intestine
34	chr4:87982600-87994000	Weak transcription	Primary T cells from cord blood	blood
35	chr4:87982600-87999600	Weak transcription	K562	blood
36	chr4:87982800-87989600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:87982800-87989800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:87982800-87990000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:87982800-87993800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr4:87982800-87994600	Weak transcription	Thymus	Thymus
41	chr4:87982800-87995000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:87983000-87988600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:87983000-87989600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:87983000-87989600	Weak transcription	Colonic Mucosa	Colon
45	chr4:87983000-87989600	Weak transcription	Gastric	stomach
46	chr4:87983000-87989800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:87983000-87989800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:87983000-87991800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:87983000-87994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:87983000-87994000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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