Variant report

Variant	rs41439544
Chromosome Location	chr15:93441931-93441932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93433692-93455675	K562	blood:	n/a	n/a
2	POLR2A	chr15:93440318-93444999	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:93440733-93444962	A549	lung:	n/a	n/a
4	POLR2A	chr15:93441370-93442561	K562	blood:	n/a	n/a
5	POLR2A	chr15:93440648-93443934	K562	blood:	n/a	n/a
6	POLR2A	chr15:93441805-93445098	U87	brain:	n/a	n/a
7	POLR2A	chr15:93441281-93442050	U87	brain:	n/a	n/a
8	POLR2A	chr15:93439531-93442863	MCF-7	breast:	n/a	n/a
9	POLR2A	chr15:93441804-93445254	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
2	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
3	chr15:93180068..93182597-chr15:93441905..93444737,2	MCF-7	breast:
4	chr15:93441494..93443862-chr3:43731000..43733877,2	MCF-7	breast:
5	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
6	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD2-6	chr15:93440954-93441977	NONHSAT049676

No data

Variant related genes	Relation type
CHD2	TF binding region
ENSG00000160746	Chromatin interaction
ENSG00000011198	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000258922	Chromatin interaction
ENSG00000258527	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16947279	0.96[AMR][1000 genomes]
rs1898914	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1898915	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58592069	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60297312	1.00[ASN][1000 genomes]
rs963719	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
8	esv1851305	chr15:93429646-93446869	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93428600-93443600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:93429400-93442400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:93430400-93442000	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:93430800-93442200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:93430800-93442200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:93430800-93443600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:93431000-93442400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:93431600-93442200	Strong transcription	Primary hematopoietic stem cells	blood
9	chr15:93431600-93442800	Strong transcription	NHDF-Ad	bronchial
10	chr15:93431600-93443000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:93431800-93442000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr15:93431800-93442200	Strong transcription	NH-A	brain
13	chr15:93431800-93442800	Strong transcription	Osteobl	bone
14	chr15:93432000-93442400	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr15:93432600-93442400	Strong transcription	HUVEC	blood vessel
16	chr15:93432600-93442600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:93432600-93443200	Weak transcription	Right Atrium	heart
18	chr15:93433200-93442000	Genic enhancers	Dnd41	blood
19	chr15:93433200-93442800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:93433400-93442200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:93434600-93442600	Strong transcription	Placenta	Placenta
22	chr15:93434800-93442200	Strong transcription	HMEC	breast
23	chr15:93435000-93442800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:93435000-93443200	Weak transcription	Stomach Mucosa	stomach
25	chr15:93436200-93443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:93436400-93443200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:93436400-93443200	Weak transcription	Ovary	ovary
28	chr15:93436600-93443200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:93436600-93443200	Weak transcription	Small Intestine	intestine
30	chr15:93436800-93442800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:93437000-93442200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
32	chr15:93437400-93443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:93437600-93443400	Weak transcription	Lung	lung
34	chr15:93437800-93443200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:93438000-93443000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:93438000-93443000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:93438000-93443200	Weak transcription	Colonic Mucosa	Colon
38	chr15:93438000-93443200	Weak transcription	Fetal Brain Male	brain
39	chr15:93438000-93443200	Weak transcription	HSMMtube	muscle
40	chr15:93438000-93443600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr15:93438200-93443000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:93438200-93443200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:93438200-93443200	Weak transcription	Right Ventricle	heart
44	chr15:93438200-93443200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:93438200-93443400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:93438200-93443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:93438200-93443400	Weak transcription	Esophagus	oesophagus
48	chr15:93438200-93444400	Weak transcription	Gastric	stomach
49	chr15:93438200-93447200	Weak transcription	Spleen	Spleen
50	chr15:93438400-93442200	Strong transcription	Primary monocytes fromperipheralblood	blood

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