Variant report

Variant	rs2009453
Chromosome Location	chr11:65399528-65399529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65399271-65399828	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:65399325-65400126	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:65399216-65399749	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:65399518-65399733	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr11:65399297-65399773	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr11:65399287-65399745	GM12892	blood:	n/a	n/a
7	POLR2A	chr11:65399401-65399757	U87	brain:	n/a	n/a
8	POLR2A	chr11:65399408-65399684	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:65399330-65399884	K562	blood:	n/a	n/a
10	POLR2A	chr11:65399495-65400229	K562	blood:	n/a	n/a
11	POLR2A	chr11:65399395-65399763	U87	brain:	n/a	n/a
12	POLR2A	chr11:65399364-65399683	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:65399474-65399738	K562	blood:	n/a	n/a
14	POLR2A	chr11:65399490-65400082	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65399412..65402464-chr11:65478309..65480936,3	MCF-7	breast:
2	chr11:65397945..65399959-chr11:65620228..65622246,2	K562	blood:

No data

Variant related genes	Relation type
MIR4690	TF binding region
ENSG00000172977	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11820062	0.81[CEU][hapmap]
rs2306364	0.82[ASW][hapmap];0.92[LWK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs523029	0.86[EUR][1000 genomes]
rs6591183	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs931127	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
6	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
8	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
9	nsv468599	chr11:65335705-65427346	ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv555213	chr11:65335705-65427346	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
11	nsv897732	chr11:65335705-65427346	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
12	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
14	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers 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	92 gene(s)	inside rSNPs	diseases
15	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
16	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
17	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' 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	227 gene(s)	inside rSNPs	diseases
18	nsv897746	chr11:65349756-65427346	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
19	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
20	esv1831135	chr11:65387352-65420872	Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	43 gene(s)	inside rSNPs	diseases
21	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2009453	SLC22A24	cis	parietal	SCAN
rs2009453	PTPRCAP	cis	cerebellum	SCAN
rs2009453	SLC22A10	cis	parietal	SCAN
rs2009453	CABP4	cis	cerebellum	SCAN
rs2009453	SLC22A9	cis	parietal	SCAN
rs2009453	SIPA1	cis	cerebellum	SCAN
rs2009453	RNASEH2C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65384400-65402200	Weak transcription	Fetal Kidney	kidney
2	chr11:65384600-65402000	Weak transcription	Psoas Muscle	Psoas
3	chr11:65384800-65399600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:65384800-65399600	Strong transcription	Ovary	ovary
5	chr11:65384800-65399800	Strong transcription	Osteobl	bone
6	chr11:65384800-65404400	Weak transcription	Fetal Heart	heart
7	chr11:65384800-65404600	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr11:65384800-65404600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr11:65384800-65404600	Strong transcription	Thymus	Thymus
10	chr11:65384800-65404800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:65384800-65404800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:65385000-65399600	Strong transcription	Rectal Smooth Muscle	rectum
13	chr11:65385000-65404200	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr11:65385000-65404200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:65385000-65404200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:65385000-65404400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:65385000-65404400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:65385000-65404400	Strong transcription	Fetal Stomach	stomach
19	chr11:65385000-65404600	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr11:65385000-65404600	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:65385000-65404800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:65385000-65405000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:65385000-65405000	Strong transcription	Brain Germinal Matrix	brain
24	chr11:65385000-65405000	Strong transcription	Fetal Brain Female	brain
25	chr11:65385000-65405000	Strong transcription	Fetal Intestine Small	intestine
26	chr11:65385200-65399600	Strong transcription	Brain Angular Gyrus	brain
27	chr11:65385200-65400800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:65385200-65401000	Strong transcription	Primary T cells from cord blood	blood
29	chr11:65385200-65402400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:65385200-65403600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:65385200-65403800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:65385200-65403800	Strong transcription	Placenta	Placenta
33	chr11:65385200-65404200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr11:65385200-65404400	Strong transcription	NHLF	lung
35	chr11:65385200-65404600	Strong transcription	Adipose Nuclei	Adipose
36	chr11:65385200-65404600	Strong transcription	Brain Anterior Caudate	brain
37	chr11:65385200-65404600	Strong transcription	Fetal Intestine Large	intestine
38	chr11:65385200-65404600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:65385200-65404600	Strong transcription	A549	lung
40	chr11:65385200-65404800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:65385200-65404800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr11:65385200-65404800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr11:65385400-65400600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr11:65385400-65404200	Strong transcription	Fetal Muscle Leg	muscle
45	chr11:65385400-65404400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:65385400-65404600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr11:65385400-65404600	Strong transcription	Fetal Thymus	thymus
48	chr11:65385600-65404600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:65385600-65404800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr11:65385800-65400800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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