Variant report

Variant	rs578270
Chromosome Location	chr11:65157820-65157821
allele	A/G
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	POLR2A	chr11:65156197-65158054	K562	blood:	n/a	n/a
2	POLR2A	chr11:65157796-65159027	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65156578..65159572-chr11:65170803..65173181,2	K562	blood:
2	chr11:65101004..65102696-chr11:65157501..65160139,2	MCF-7	breast:
3	chr11:65156137..65158686-chr11:65238471..65240307,2	K562	blood:

Variant related genes	Relation type
FRMD8	TF binding region
ENSG00000133884	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2073799	0.86[EUR][1000 genomes]
rs2073800	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930154	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547221	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs651283	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs652501	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666194	0.86[GIH][hapmap]
rs681309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers 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	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
15	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs578270	SLC22A24	cis	parietal	SCAN
rs578270	CDK2AP2	cis	cerebellum	SCAN
rs578270	TPCN2	cis	parietal	SCAN
rs578270	HRASLS2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65154800-65161000	Weak transcription	Aorta	Aorta
2	chr11:65154800-65164800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:65155000-65158000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr11:65155000-65158000	Genic enhancers	Fetal Intestine Small	intestine
5	chr11:65155000-65158200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:65155000-65158400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr11:65155000-65158600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:65155000-65158800	Enhancers	Brain Cingulate Gyrus	brain
9	chr11:65155000-65159000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:65155000-65159000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr11:65155000-65162000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:65155200-65158800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:65155400-65159400	Enhancers	Left Ventricle	heart
14	chr11:65155600-65158000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr11:65155600-65158200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr11:65155600-65158400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:65155600-65159800	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr11:65155600-65159800	Genic enhancers	Fetal Muscle Leg	muscle
19	chr11:65155600-65161800	Genic enhancers	Spleen	Spleen
20	chr11:65155600-65162400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:65155800-65158000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:65155800-65158200	Genic enhancers	Fetal Thymus	thymus
23	chr11:65155800-65158400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:65155800-65158800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:65155800-65158800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:65155800-65158800	Transcr. at gene 5' and 3'	Esophagus	oesophagus
27	chr11:65155800-65158800	Enhancers	Fetal Brain Female	brain
28	chr11:65155800-65159600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:65156000-65158200	Genic enhancers	Monocytes-CD14+_RO01746	blood
30	chr11:65156000-65158800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:65156000-65158800	Genic enhancers	Colonic Mucosa	Colon
32	chr11:65156000-65159800	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr11:65156000-65162200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:65156200-65158200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:65156200-65158600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr11:65156200-65159800	Genic enhancers	Lung	lung
37	chr11:65156400-65158000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:65156400-65158000	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr11:65156400-65158200	Enhancers	NH-A	brain
40	chr11:65156400-65158600	Genic enhancers	Fetal Intestine Large	intestine
41	chr11:65156400-65158800	Enhancers	Ovary	ovary
42	chr11:65156400-65159000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr11:65156400-65159000	Enhancers	NHDF-Ad	bronchial
44	chr11:65156400-65159600	Genic enhancers	Fetal Stomach	stomach
45	chr11:65156600-65158600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:65156600-65158600	Genic enhancers	Rectal Mucosa Donor 29	rectum
47	chr11:65156600-65158800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:65156600-65159000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:65156600-65159000	Enhancers	Brain Angular Gyrus	brain
50	chr11:65156600-65159200	Weak transcription	Liver	Liver

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