Variant report

Variant	rs236996
Chromosome Location	chr4:88005203-88005204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87929301..87933851-chr4:88000404..88005339,4	K562	blood:
2	chr4:87927747..87929657-chr4:88004396..88007701,4	MCF-7	breast:
3	chr4:88002713..88005662-chr4:88048003..88049629,2	K562	blood:
4	chr4:88004411..88007536-chr4:88008930..88011901,3	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10023050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[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];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097127	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11946481	0.82[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	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[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	0.93[AMR][1000 genomes];0.87[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];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2125787	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];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236984	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236985	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]
rs236987	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28432336	0.84[ASN][1000 genomes]
rs28677145	0.80[AMR][1000 genomes];0.82[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];0.93[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];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342453	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342454	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.92[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];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736669	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775217	0.90[AMR][1000 genomes];0.86[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];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775221	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775223	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs442177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447990	0.81[MKK][hapmap]
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];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72877984	0.82[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];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9998251	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[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
rs236996	AFF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87990200-88008000	Weak transcription	Spleen	Spleen
2	chr4:87995200-88009400	Weak transcription	HepG2	liver
3	chr4:87995200-88010600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:87995400-88006200	Weak transcription	Hela-S3	cervix
6	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:87995600-88011200	Weak transcription	Colonic Mucosa	Colon
8	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:87996000-88005400	Weak transcription	Primary T cells from cord blood	blood
10	chr4:87996000-88005400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr4:87996000-88005800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr4:87998800-88008000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:87999000-88005400	Enhancers	Adipose Nuclei	Adipose
15	chr4:87999400-88006000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:87999400-88007600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:87999400-88010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:87999600-88006400	Enhancers	Rectal Smooth Muscle	rectum
19	chr4:87999600-88008200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:87999600-88010600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:87999600-88011000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:87999800-88007000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:88000000-88007000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:88000200-88005400	Enhancers	Colon Smooth Muscle	Colon
25	chr4:88000200-88010600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:88000400-88007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:88000600-88006600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr4:88000600-88008400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:88000600-88013000	Weak transcription	A549	lung
31	chr4:88000800-88005400	Weak transcription	Fetal Intestine Large	intestine
32	chr4:88000800-88006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:88000800-88008400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:88001000-88006200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:88001200-88007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:88001200-88011400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:88001400-88006000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:88001400-88013800	Weak transcription	HSMM	muscle
39	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:88001600-88005800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:88001600-88008200	Weak transcription	Fetal Kidney	kidney
42	chr4:88001600-88014000	Weak transcription	Small Intestine	intestine
43	chr4:88001800-88006800	Weak transcription	Fetal Intestine Small	intestine
44	chr4:88001800-88008200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:88001800-88010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:88001800-88011800	Weak transcription	Fetal Stomach	stomach
47	chr4:88001800-88013200	Weak transcription	Stomach Mucosa	stomach
48	chr4:88001800-88013400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:88001800-88013800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:88001800-88025200	Weak transcription	Gastric	stomach

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