Variant report

Variant	rs11853859
Chromosome Location	chr15:74890842-74890843
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74885278..74889186-chr15:74890286..74893326,4	K562	blood:
2	chr15:74885692..74889192-chr15:74889315..74893477,4	MCF-7	breast:
3	chr15:74882811..74885228-chr15:74890404..74892323,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLK3-1	chr15:74890841-74891878	NONHSAT047251

Variant related genes	Relation type
ENSG00000179361	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12439944	1.00[CEU][hapmap]
rs12593213	1.00[CEU][hapmap]
rs12593251	1.00[CEU][hapmap]
rs16972714	1.00[CEU][hapmap]
rs2072649	0.82[CHB][hapmap]
rs3743484	1.00[CEU][hapmap]
rs3803461	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825943	1.00[CEU][hapmap]
rs56298217	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7497749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1812223	chr15:74869438-74948063	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv1814078	chr15:74884447-74948063	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv457204	chr15:74885091-74948063	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv569991	chr15:74885091-74948063	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv542434	chr15:74885329-74929552	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1047943	chr15:74885329-74940857	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv976950	chr15:74888247-74891372	Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv817698	chr15:74889163-75019449	Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74881200-74892200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:74881400-74892200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:74883400-74892000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:74886000-74891000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:74888200-74893800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:74890200-74891200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:74890400-74891000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr15:74890400-74891000	Flanking Active TSS	GM12878-XiMat	blood
9	chr15:74890400-74891200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:74890400-74891600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr15:74890400-74891600	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr15:74890400-74891600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:74890400-74891600	Flanking Active TSS	Fetal Thymus	thymus
14	chr15:74890400-74891600	Flanking Active TSS	NHEK	skin
15	chr15:74890400-74891800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:74890400-74891800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr15:74890400-74891800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr15:74890400-74891800	Flanking Active TSS	Hela-S3	cervix
19	chr15:74890400-74891800	Flanking Active TSS	HepG2	liver
20	chr15:74890400-74892000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:74890400-74892000	Flanking Active TSS	Dnd41	blood
22	chr15:74890400-74892000	Flanking Active TSS	K562	blood
23	chr15:74890400-74892200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:74890400-74892200	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr15:74890400-74892400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr15:74890400-74892400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr15:74890600-74891000	Active TSS	Primary T cells from cord blood	blood
28	chr15:74890600-74891000	Active TSS	Primary hematopoietic stem cells	blood
29	chr15:74890600-74891000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:74890600-74891200	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr15:74890600-74891200	Active TSS	Thymus	Thymus
32	chr15:74890600-74891200	Flanking Active TSS	HMEC	breast
33	chr15:74890600-74891400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:74890600-74891400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:74890600-74891400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:74890600-74891400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:74890600-74891400	Active TSS	Brain Hippocampus Middle	brain
38	chr15:74890600-74891400	Active TSS	Colon Smooth Muscle	Colon
39	chr15:74890600-74891400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr15:74890600-74891400	Active TSS	Fetal Brain Female	brain
41	chr15:74890600-74891400	Active TSS	Fetal Intestine Large	intestine
42	chr15:74890600-74891600	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr15:74890600-74891600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:74890600-74891600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr15:74890600-74891600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr15:74890600-74891600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:74890600-74891600	Active TSS	Brain Germinal Matrix	brain
48	chr15:74890600-74891800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr15:74890600-74891800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:74890600-74891800	Active TSS	Brain Angular Gyrus	brain

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