Variant report

Variant	rs624975
Chromosome Location	chr11:64576954-64576955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr11:64576935-64576993	Hela-S3	cervix:	n/a	n/a
2	MAZ	chr11:64576924-64578651	IMR90	lung:	n/a	chr11:64577872-64577882 chr11:64578551-64578560 chr11:64578547-64578562 chr11:64578551-64578558 chr11:64578550-64578561 chr11:64578550-64578561
3	POLR2A	chr11:64576953-64578553	SK-N-MC	brain:	n/a	n/a
4	MXI1	chr11:64576859-64578783	SK-N-SH	brain:	n/a	n/a
5	HCFC1	chr11:64576669-64578793	Hela-S3	cervix:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64575827..64578000-chr11:64862581..64864116,2	MCF-7	breast:
2	chr11:64575575..64578460-chr11:64644399..64646025,3	MCF-7	breast:
3	chr11:64563150..64565307-chr11:64574970..64577233,2	K562	blood:
4	chr11:64575180..64578002-chr11:65268196..65269989,2	K562	blood:
5	chr11:64561801..64564643-chr11:64576528..64579219,3	MCF-7	breast:
6	chr11:64574843..64581404-chr11:64607394..64613763,11	MCF-7	breast:
7	chr11:64575754..64580490-chr11:64608432..64614008,12	MCF-7	breast:
8	chr11:64576838..64579724-chr11:64644602..64648695,4	K562	blood:
9	chr11:64544159..64547610-chr11:64575495..64579776,5	K562	blood:
10	chr11:64576171..64577723-chr11:64862076..64864816,2	K562	blood:
11	chr11:64526958..64529001-chr11:64574985..64577155,2	MCF-7	breast:
12	chr11:64576576..64578082-chr11:65296223..65299192,2	MCF-7	breast:
13	chr11:64574624..64577319-chr11:64601791..64604479,3	MCF-7	breast:
14	chr11:64543661..64548104-chr11:64572931..64579605,12	MCF-7	breast:
15	chr11:64576531..64579028-chr11:64877071..64879656,2	MCF-7	breast:
16	chr11:64575458..64578440-chr11:64655373..64657012,2	MCF-7	breast:

No data

Variant related genes	Relation type
MEN1	TF binding region
ENSG00000251562	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000168067	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000142186	Chromatin interaction
ENSG00000068976	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000149809	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10897525	0.88[MEX][hapmap]
rs11231859	0.90[CEU][hapmap];0.83[MEX][hapmap]
rs11231869	0.88[MEX][hapmap]
rs1143937	0.90[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1633462	0.89[CEU][hapmap]
rs17146121	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs2073798	0.81[GIH][hapmap]
rs2267918	0.90[CEU][hapmap];0.83[MEX][hapmap]
rs2284301	0.90[CEU][hapmap];0.83[MEX][hapmap]
rs2959652	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs3741398	0.90[CEU][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs3809076	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs474707	0.82[GIH][hapmap];0.89[MEX][hapmap]
rs477549	0.90[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs483962	0.90[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs487105	0.90[CEU][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs489192	0.90[CEU][hapmap]
rs496914	0.90[CEU][hapmap]
rs509606	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs523200	0.90[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap]
rs532747	0.88[MEX][hapmap]
rs547066	0.80[GIH][hapmap];0.87[MEX][hapmap]
rs559566	0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs569602	0.88[MEX][hapmap]
rs589691	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs600347	0.93[ASN][1000 genomes]
rs606458	0.90[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap]
rs607389	0.90[CEU][hapmap]
rs625172	0.81[GIH][hapmap]
rs637332	0.90[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs669976	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677298	0.90[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs67808744	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680273	0.90[CEU][hapmap];0.84[MEX][hapmap]
rs693235	0.81[CEU][hapmap]
rs7939965	0.80[CEU][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
4	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
5	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
8	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
9	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
10	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
11	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
12	nsv832189	chr11:64487183-64620199	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
13	nsv469962	chr11:64527080-64621573	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
14	nsv897702	chr11:64532579-64584231	Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
15	nsv519478	chr11:64546391-64584987	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs624975	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs624975	SF1	cis	multi-tissue	Pritchard
rs624975	SF1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64571400-64577000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:64571800-64577000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:64571800-64577000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:64571800-64577000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:64571800-64577000	Weak transcription	HSMMtube	muscle
6	chr11:64572000-64577000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:64572000-64577000	Weak transcription	Small Intestine	intestine
8	chr11:64572000-64577400	Weak transcription	Aorta	Aorta
9	chr11:64573800-64577000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:64575200-64577000	Weak transcription	NHDF-Ad	bronchial
11	chr11:64575800-64577000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:64575800-64577200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:64576000-64577000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:64576000-64577000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:64576000-64577000	Enhancers	Fetal Brain Male	brain
16	chr11:64576000-64577000	Enhancers	Stomach Smooth Muscle	stomach
17	chr11:64576400-64577200	Enhancers	Primary B cells from peripheral blood	blood
18	chr11:64576400-64577200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr11:64576400-64577200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:64576400-64577400	Flanking Active TSS	Fetal Brain Female	brain
21	chr11:64576600-64577000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr11:64576600-64577000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:64576600-64577000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr11:64576600-64577000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr11:64576600-64577000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr11:64576600-64577000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr11:64576600-64577000	Genic enhancers	Fetal Muscle Leg	muscle
28	chr11:64576600-64577000	Enhancers	Fetal Thymus	thymus
29	chr11:64576600-64577000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr11:64576600-64577600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:64576800-64577000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:64576800-64577000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:64576800-64577000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:64576800-64577000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:64576800-64577000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:64576800-64577000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:64576800-64577000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:64576800-64577000	Enhancers	Primary B cells from cord blood	blood
39	chr11:64576800-64577000	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr11:64576800-64577000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:64576800-64577000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:64576800-64577000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:64576800-64577000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr11:64576800-64577000	Active TSS	Brain Angular Gyrus	brain
45	chr11:64576800-64577000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr11:64576800-64577000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:64576800-64577000	Enhancers	Colon Smooth Muscle	Colon
48	chr11:64576800-64577000	Enhancers	Duodenum Mucosa	Duodenum
49	chr11:64576800-64577000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr11:64576800-64577000	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links