Variant report

Variant	rs1143937
Chromosome Location	chr11:64569000-64569001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr11:64568891-64569014	GM12878	blood:	n/a	n/a
2	EBF1	chr11:64568476-64569264	GM12878	blood:	n/a	chr11:64569063-64569074 chr11:64569034-64569044 chr11:64569033-64569044
3	EBF1	chr11:64568627-64569263	GM12878	blood:	n/a	chr11:64569063-64569074 chr11:64569034-64569044 chr11:64569033-64569044
4	POLR2A	chr11:64568555-64569079	GM12878	blood:	n/a	n/a
5	ELF1	chr11:64568574-64570677	GM12878	blood:	n/a	chr11:64569343-64569354 chr11:64569377-64569390 chr11:64569341-64569354
6	WRNIP1	chr11:64568849-64569089	GM12878	blood:	n/a	n/a
7	MTA3	chr11:64568560-64570486	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:64568643-64569790	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64567558..64572906-chr11:64572928..64575629,5	MCF-7	breast:
2	chr11:64542437..64548103-chr11:64565883..64573066,9	K562	blood:
3	chr11:64556614..64564048-chr11:64568895..64571879,7	MCF-7	breast:
4	chr11:64568225..64570801-chr11:64644714..64647592,2	MCF-7	breast:
5	chr11:64568677..64572675-chr11:64611050..64613930,4	K562	blood:
6	chr11:64568638..64571349-chr11:64644530..64646635,3	MCF-7	breast:
7	chr11:64543298..64549423-chr11:64566945..64572163,10	K562	blood:
8	chr11:64544683..64548200-chr11:64565443..64572182,16	MCF-7	breast:
9	chr11:64568489..64574764-chr11:64609155..64613913,19	MCF-7	breast:
10	chr11:64568159..64573413-chr11:64882450..64885409,5	K562	blood:
11	chr11:64568549..64570067-chr11:64641027..64643704,2	K562	blood:
12	chr11:64562935..64566050-chr11:64567967..64570422,3	K562	blood:
13	chr11:64568984..64570797-chr11:64610874..64612678,2	K562	blood:
14	chr11:64568687..64571472-chr11:64762371..64764508,2	K562	blood:

Variant related genes	Relation type
MAP4K2	TF binding region
ENSG00000168066	Chromatin interaction
ENSG00000168062	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000133895	Chromatin interaction
ENSG00000168067	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000255173	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10897525	0.88[MEX][hapmap]
rs11231853	0.86[CEU][hapmap]
rs11231859	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs11231869	0.88[MEX][hapmap]
rs1633462	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs17146121	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs2267918	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs2284301	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs2959652	1.00[CEU][hapmap]
rs3741398	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs3809076	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs474707	0.81[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs476037	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs477549	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs483962	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs487105	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes]
rs489192	1.00[CEU][hapmap]
rs490980	0.89[CEU][hapmap]
rs496914	1.00[CEU][hapmap]
rs509606	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs523200	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs532747	0.88[MEX][hapmap]
rs547066	0.87[MEX][hapmap]
rs559566	0.81[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs569602	0.88[MEX][hapmap]
rs582980	0.81[EUR][1000 genomes]
rs589691	1.00[CEU][hapmap]
rs593394	0.81[AMR][1000 genomes]
rs600347	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs606458	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs607389	1.00[CEU][hapmap]
rs624975	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]
rs637332	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs669976	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677298	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67808744	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs680273	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs693235	0.90[CEU][hapmap]
rs7939965	0.89[CEU][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv897703	chr11:64538346-64574200	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
18	nsv519117	chr11:64546391-64573589	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	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
20	nsv555204	chr11:64561200-64574200	Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv555205	chr11:64561200-64575505	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	nsv555206	chr11:64563757-64574200	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1143937	SF1	cis	multi-tissue	Pritchard
rs1143937	SF1	cis	lymphoblastoid	seeQTL
rs1143937	SF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:136 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64547200-64569600	Weak transcription	Small Intestine	intestine
2	chr11:64547200-64569600	Weak transcription	NH-A	brain
3	chr11:64547200-64569800	Weak transcription	Osteobl	bone
4	chr11:64547200-64570000	Weak transcription	Fetal Kidney	kidney
5	chr11:64547400-64569600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:64547400-64569800	Weak transcription	NHEK	skin
7	chr11:64547600-64569800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:64550200-64569400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:64550400-64570000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:64555400-64569400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:64555400-64570000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:64555600-64569000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:64555600-64569800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:64555800-64569000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:64556000-64569000	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:64557800-64569600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr11:64558000-64569000	Strong transcription	Fetal Intestine Small	intestine
18	chr11:64558200-64570000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:64561400-64569400	Weak transcription	Stomach Mucosa	stomach
20	chr11:64561600-64570000	Weak transcription	Fetal Heart	heart
21	chr11:64562000-64570000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:64562000-64570000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:64563000-64569600	Weak transcription	NHDF-Ad	bronchial
24	chr11:64564000-64569000	Weak transcription	Fetal Lung	lung
25	chr11:64564000-64570000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:64564200-64569800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr11:64564400-64569800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:64564400-64570000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:64564600-64569800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:64564800-64569200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:64565000-64569400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:64565000-64569400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:64565000-64569600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:64565000-64569600	Weak transcription	Fetal Brain Female	brain
35	chr11:64565000-64569800	Weak transcription	Brain Angular Gyrus	brain
36	chr11:64565000-64570200	Weak transcription	Aorta	Aorta
37	chr11:64565200-64570000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:64565200-64570000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:64565200-64570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:64566000-64569200	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr11:64566200-64569000	Genic enhancers	Spleen	Spleen
42	chr11:64566200-64570000	Enhancers	K562	blood
43	chr11:64566600-64569000	Genic enhancers	Primary T cells from cord blood	blood
44	chr11:64566800-64569600	Weak transcription	Liver	Liver
45	chr11:64566800-64569800	Weak transcription	Brain Substantia Nigra	brain
46	chr11:64567000-64569200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:64567000-64569200	Enhancers	HUVEC	blood vessel
48	chr11:64567000-64569600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:64567200-64569000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr11:64567200-64569200	Genic enhancers	Primary T cells fromperipheralblood	blood

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