Variant report

Variant	rs342438
Chromosome Location	chr4:88040406-88040407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87854962..87858816-chr4:88038072..88042352,4	MCF-7	breast:
2	chr4:88039768..88041712-chr4:88052225..88054445,2	K562	blood:
3	chr4:88027865..88029794-chr4:88040230..88042955,3	MCF-7	breast:
4	chr4:88037805..88040790-chr4:88041752..88044910,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10023050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1037814	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097127	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1408	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1674999	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16930	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17012368	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2045592	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2125787	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];0.93[ASN][1000 genomes]
rs236984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236985	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]
rs236987	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236996	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]
rs2926511	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs342435	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs342437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342453	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342454	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs342467	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs342468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs342469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736669	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3775214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775217	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775220	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775221	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775223	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs442177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs447990	0.80[LWK][hapmap]
rs4693156	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7660883	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs9998251	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs342438	AFF1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:88026200-88042200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr4:88026400-88042400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:88026400-88063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:88026600-88042200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr4:88026600-88042600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr4:88026600-88055600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:88029800-88041600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:88030000-88048800	Weak transcription	A549	lung
10	chr4:88030600-88041200	Weak transcription	HSMMtube	muscle
11	chr4:88030600-88041600	Weak transcription	NH-A	brain
12	chr4:88030600-88057600	Weak transcription	Brain Germinal Matrix	brain
13	chr4:88032800-88040600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:88032800-88041400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr4:88032800-88041400	Strong transcription	Fetal Intestine Large	intestine
16	chr4:88032800-88041600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr4:88032800-88041800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr4:88032800-88043200	Strong transcription	Primary B cells from cord blood	blood
19	chr4:88032800-88043600	Strong transcription	Fetal Thymus	thymus
20	chr4:88032800-88059000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:88033000-88040600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:88033000-88042800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr4:88033200-88040600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:88033200-88041800	Strong transcription	Thymus	Thymus
25	chr4:88033600-88041400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:88033600-88042200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:88033600-88047600	Weak transcription	HSMM	muscle
28	chr4:88034200-88041200	Strong transcription	Fetal Intestine Small	intestine
29	chr4:88034200-88042200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:88034400-88042000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:88034800-88043400	Weak transcription	Hela-S3	cervix
32	chr4:88035400-88042200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr4:88035600-88041600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:88035600-88041600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr4:88035600-88056800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr4:88035600-88063800	Strong transcription	Primary T cells from cord blood	blood
37	chr4:88035800-88041800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:88035800-88042000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:88035800-88042000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:88036000-88043000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr4:88036400-88063600	Weak transcription	Fetal Brain Male	brain
42	chr4:88036600-88040600	Weak transcription	Aorta	Aorta
43	chr4:88036600-88041400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:88036800-88041800	Weak transcription	Stomach Mucosa	stomach
45	chr4:88036800-88046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:88036800-88046800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:88036800-88059200	Weak transcription	Fetal Brain Female	brain
48	chr4:88037000-88042600	Weak transcription	NHLF	lung
49	chr4:88037400-88041800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr4:88037600-88040800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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