Variant report

Variant	rs340636
Chromosome Location	chr4:87930760-87930761
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87867281..87868896-chr4:87929541..87932174,2	MCF-7	breast:
2	chr4:87929393..87932319-chr4:87992706..87994245,2	K562	blood:
3	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
4	chr4:87929301..87933851-chr4:88000404..88005339,4	K562	blood:
5	chr4:87862443..87864681-chr4:87929416..87931168,2	MCF-7	breast:
6	chr4:87832559..87834802-chr4:87929759..87932272,2	K562	blood:
7	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000235043	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10015639	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10032244	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11729622	0.97[ASN][1000 genomes]
rs12651081	0.90[LWK][hapmap]
rs13126334	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13127250	0.98[ASN][1000 genomes]
rs1471251	0.82[CEU][hapmap]
rs2007132	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2053769	0.84[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2053770	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28495007	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113494	0.85[LWK][hapmap]
rs340626	0.90[ASN][1000 genomes]
rs340630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs340633	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs340637	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs340638	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs340639	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs340641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340642	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs340643	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs340648	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs340650	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs340651	0.93[ASN][1000 genomes]
rs375795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs388401	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]
rs4274814	0.90[LWK][hapmap]
rs4386567	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs443459	0.90[ASN][1000 genomes]
rs4536898	0.90[LWK][hapmap]
rs4693796	0.83[ASN][1000 genomes]
rs4693798	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693800	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58633957	0.90[ASN][1000 genomes]
rs6531941	0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6531946	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6531948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811587	0.99[ASN][1000 genomes]
rs6839933	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs867196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9715807	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs340636	AFF1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87927600-87932200	Active TSS	GM12878-XiMat	blood
2	chr4:87928600-87931200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr4:87928800-87931000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr4:87928800-87931800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr4:87928800-87931800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:87929200-87930800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:87929200-87930800	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr4:87929200-87931000	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr4:87929200-87931000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr4:87929200-87931000	Flanking Active TSS	Dnd41	blood
11	chr4:87929200-87931000	Flanking Active TSS	HUVEC	blood vessel
12	chr4:87929200-87931200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr4:87929200-87931600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:87929200-87934200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:87929200-87939400	Weak transcription	Gastric	stomach
16	chr4:87929400-87931200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:87929400-87946200	Weak transcription	Esophagus	oesophagus
18	chr4:87929600-87930800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:87929600-87931200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:87929600-87931200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:87929600-87931400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:87929600-87931400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr4:87929600-87931600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:87929600-87931600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr4:87929600-87931600	Enhancers	Stomach Mucosa	stomach
26	chr4:87929600-87932200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr4:87929600-87932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:87929600-87933200	Enhancers	Brain Substantia Nigra	brain
29	chr4:87929600-87934000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:87929600-87935000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:87929600-87935400	Weak transcription	HSMM	muscle
32	chr4:87929600-87937000	Enhancers	Fetal Heart	heart
33	chr4:87929600-87938000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:87929600-87938800	Weak transcription	HSMMtube	muscle
35	chr4:87929800-87930800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr4:87929800-87931000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:87929800-87931000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr4:87929800-87931200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr4:87929800-87932000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:87929800-87932400	Weak transcription	NH-A	brain
41	chr4:87929800-87932600	Enhancers	A549	lung
42	chr4:87929800-87933600	Enhancers	HepG2	liver
43	chr4:87929800-87936600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr4:87929800-87937000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:87930000-87930800	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr4:87930000-87930800	Enhancers	Fetal Muscle Leg	muscle
47	chr4:87930000-87931000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr4:87930000-87931000	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr4:87930000-87931000	Flanking Active TSS	Psoas Muscle	Psoas
50	chr4:87930000-87931000	Enhancers	Sigmoid Colon	Sigmoid Colon

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