Variant report

Variant	rs236985
Chromosome Location	chr4:88008782-88008783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88005383..88008853-chr4:88008930..88010972,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10023050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1037814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097127	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11946481	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1408	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1674999	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs17012368	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2045592	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2125787	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236987	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236996	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28432336	0.84[ASN][1000 genomes]
rs28677145	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2926511	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs342435	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs342437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342453	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342454	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736669	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775217	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775220	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775221	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775223	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs442177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693156	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72877984	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7660883	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9998251	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
rs236985	AFF1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995200-88009400	Weak transcription	HepG2	liver
2	chr4:87995200-88010600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:87995600-88011200	Weak transcription	Colonic Mucosa	Colon
6	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:87999400-88010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:87999600-88010600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:87999600-88011000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:88000200-88010600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:88000600-88013000	Weak transcription	A549	lung
14	chr4:88001200-88011400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:88001400-88013800	Weak transcription	HSMM	muscle
16	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:88001600-88014000	Weak transcription	Small Intestine	intestine
18	chr4:88001800-88010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:88001800-88011800	Weak transcription	Fetal Stomach	stomach
20	chr4:88001800-88013200	Weak transcription	Stomach Mucosa	stomach
21	chr4:88001800-88013400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:88001800-88013800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:88001800-88025200	Weak transcription	Gastric	stomach
24	chr4:88002000-88009800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
26	chr4:88003600-88013000	Weak transcription	HMEC	breast
27	chr4:88003600-88013200	Weak transcription	Osteobl	bone
28	chr4:88004200-88010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:88004200-88019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:88004400-88025200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:88004800-88009000	Enhancers	Psoas Muscle	Psoas
32	chr4:88004800-88010400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:88005000-88008800	Strong transcription	Primary B cells from cord blood	blood
34	chr4:88005000-88017400	Strong transcription	Dnd41	blood
35	chr4:88005200-88008800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:88005400-88009400	Strong transcription	Primary T cells from cord blood	blood
37	chr4:88005800-88014000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:88006000-88008800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr4:88006200-88010600	Weak transcription	NHDF-Ad	bronchial
40	chr4:88006200-88011200	Weak transcription	Fetal Lung	lung
41	chr4:88006400-88010800	Weak transcription	K562	blood
42	chr4:88007000-88008800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:88007000-88009000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:88007000-88010400	Genic enhancers	Left Ventricle	heart
45	chr4:88007200-88009600	Enhancers	Colon Smooth Muscle	Colon
46	chr4:88007400-88009000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr4:88007400-88010000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr4:88007600-88009000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:88007600-88009600	Strong transcription	Hela-S3	cervix
50	chr4:88007600-88010400	Enhancers	Right Atrium	heart

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