Variant report

Variant	rs739390
Chromosome Location	chr11:65157239-65157240
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	POLR2A	chr11:65156437-65157579	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:65156197-65158054	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65116402..65157784-chr11:65261420..65278410,154	K562	blood:
2	chr11:65156578..65159572-chr11:65170803..65173181,2	K562	blood:
3	chr11:65155994..65157611-chr11:65308112..65310135,2	MCF-7	breast:
4	chr11:65156137..65158686-chr11:65238471..65240307,2	K562	blood:

Variant related genes	Relation type
FRMD8	TF binding region
ENSG00000270117	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000251562	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10128627	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12417665	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12799896	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35410259	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741389	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482320	1.00[YRI][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	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
rs739390	RPS6KB2	cis	parietal	SCAN
rs739390	TPCN2	cis	parietal	SCAN
rs739390	COX8A	cis	parietal	SCAN
rs739390	TncRNA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65154800-65157400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65154800-65157400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr11:65154800-65157400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:65154800-65157800	Weak transcription	Fetal Heart	heart
5	chr11:65154800-65161000	Weak transcription	Aorta	Aorta
6	chr11:65154800-65164800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:65155000-65157400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:65155000-65157400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:65155000-65157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:65155000-65157400	Weak transcription	Fetal Lung	lung
11	chr11:65155000-65157600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:65155000-65157600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr11:65155000-65157800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:65155000-65157800	Enhancers	HepG2	liver
15	chr11:65155000-65158000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr11:65155000-65158000	Genic enhancers	Fetal Intestine Small	intestine
17	chr11:65155000-65158200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:65155000-65158400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr11:65155000-65158600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:65155000-65158800	Enhancers	Brain Cingulate Gyrus	brain
21	chr11:65155000-65159000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:65155000-65159000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr11:65155000-65162000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:65155200-65157400	Genic enhancers	Thymus	Thymus
25	chr11:65155200-65157600	Enhancers	HUVEC	blood vessel
26	chr11:65155200-65158800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:65155400-65157600	Enhancers	Stomach Mucosa	stomach
28	chr11:65155400-65159400	Enhancers	Left Ventricle	heart
29	chr11:65155600-65157400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr11:65155600-65157600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:65155600-65157600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr11:65155600-65157600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
33	chr11:65155600-65157800	Transcr. at gene 5' and 3'	Hela-S3	cervix
34	chr11:65155600-65158000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr11:65155600-65158200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr11:65155600-65158400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:65155600-65159800	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr11:65155600-65159800	Genic enhancers	Fetal Muscle Leg	muscle
39	chr11:65155600-65161800	Genic enhancers	Spleen	Spleen
40	chr11:65155600-65162400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:65155800-65157400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr11:65155800-65157400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
43	chr11:65155800-65157800	Genic enhancers	Brain Hippocampus Middle	brain
44	chr11:65155800-65157800	Genic enhancers	Placenta	Placenta
45	chr11:65155800-65157800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
46	chr11:65155800-65158000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:65155800-65158200	Genic enhancers	Fetal Thymus	thymus
48	chr11:65155800-65158400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:65155800-65158800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr11:65155800-65158800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin

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