Variant report

Variant	rs10897525
Chromosome Location	chr11:64552946-64552947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64544768..64548246-chr11:64552203..64559348,13	K562	blood:
2	11:64544826-64559210..11:64658316-64660295	GM12878	blood:
3	chr11:64552248..64555087-chr11:64879358..64881894,2	MCF-7	breast:
4	chr11:64552481..64554054-chr11:64570042..64572639,2	MCF-7	breast:
5	chr11:64550295..64559770-chr11:64606799..64612778,15	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP4K2-2	chr11:64552393-64553092	ENSG00000269290.1

Variant related genes	Relation type
ENSG00000229719	Chromatin interaction
ENSG00000207648	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000267804	Chromatin interaction
ENSG00000168067	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000269038	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11231859	0.83[MEX][hapmap]
rs11231869	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs1143937	0.88[MEX][hapmap]
rs12223914	0.81[AMR][1000 genomes]
rs17146121	0.88[MEX][hapmap]
rs2267918	0.83[MEX][hapmap]
rs2284301	0.83[MEX][hapmap]
rs2285341	1.00[EUR][1000 genomes]
rs3741398	0.94[MEX][hapmap]
rs3759049	1.00[EUR][1000 genomes]
rs3809076	0.88[MEX][hapmap]
rs474707	0.89[MEX][hapmap]
rs476037	0.88[MEX][hapmap]
rs477549	0.89[MEX][hapmap]
rs483962	0.89[MEX][hapmap]
rs487105	0.94[MEX][hapmap]
rs523200	0.84[MEX][hapmap]
rs532747	0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs547066	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs569602	0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs606458	0.84[MEX][hapmap]
rs624975	0.88[MEX][hapmap]
rs637332	0.89[MEX][hapmap]
rs669976	0.88[MEX][hapmap]
rs677298	0.84[JPT][hapmap];0.83[MEX][hapmap]
rs680273	0.84[MEX][hapmap]
rs686171	0.84[AMR][1000 genomes]
rs7939965	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers 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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10897525	SF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64546000-64556000	Weak transcription	Gastric	stomach
2	chr11:64546200-64556200	Weak transcription	Ovary	ovary
3	chr11:64546400-64555800	Weak transcription	Lung	lung
4	chr11:64546600-64555400	Weak transcription	Spleen	Spleen
5	chr11:64547200-64553800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:64547200-64553800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:64547200-64554600	Weak transcription	Fetal Brain Male	brain
8	chr11:64547200-64555000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:64547200-64555000	Weak transcription	Brain Angular Gyrus	brain
10	chr11:64547200-64555200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:64547200-64555800	Weak transcription	Fetal Lung	lung
12	chr11:64547200-64556000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:64547200-64556200	Weak transcription	Esophagus	oesophagus
14	chr11:64547200-64556400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:64547200-64556600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:64547200-64556600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:64547200-64557200	Weak transcription	Aorta	Aorta
18	chr11:64547200-64557400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:64547200-64561000	Weak transcription	Fetal Heart	heart
20	chr11:64547200-64563200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:64547200-64569600	Weak transcription	Small Intestine	intestine
22	chr11:64547200-64569600	Weak transcription	NH-A	brain
23	chr11:64547200-64569800	Weak transcription	Osteobl	bone
24	chr11:64547200-64570000	Weak transcription	Fetal Kidney	kidney
25	chr11:64547400-64553800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:64547400-64553800	Weak transcription	Brain Germinal Matrix	brain
27	chr11:64547400-64555000	Weak transcription	Liver	Liver
28	chr11:64547400-64555000	Weak transcription	Brain Substantia Nigra	brain
29	chr11:64547400-64555200	Weak transcription	A549	lung
30	chr11:64547400-64556000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:64547400-64556000	Weak transcription	Adipose Nuclei	Adipose
32	chr11:64547400-64556000	Weak transcription	Brain Anterior Caudate	brain
33	chr11:64547400-64556200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:64547400-64556200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:64547400-64557000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:64547400-64557200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:64547400-64557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:64547400-64557400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:64547400-64557400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:64547400-64563200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:64547400-64563200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr11:64547400-64563800	Weak transcription	NHLF	lung
43	chr11:64547400-64569600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:64547400-64569800	Weak transcription	NHEK	skin
45	chr11:64547600-64553800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr11:64547600-64553800	Weak transcription	Fetal Intestine Small	intestine
47	chr11:64547600-64555000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:64547600-64555000	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:64547600-64555000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:64547600-64555200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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