Variant report

Variant	rs17704838
Chromosome Location	chr15:93448883-93448884
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:93448445..93452273-chr15:93477513..93479275,3	K562	blood:
2	chr15:93448445..93451648-chr15:93477513..93481560,4	K562	blood:
3	chr15:93368093..93370733-chr15:93448780..93451339,2	K562	blood:
4	chr15:93447178..93449882-chr15:93481801..93484893,3	K562	blood:
5	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
6	chr15:93447864..93450359-chr15:93471723..93473623,2	K562	blood:
7	chr15:93447178..93448991-chr15:93481801..93483566,2	K562	blood:
8	chr15:93448445..93450159-chr15:93483633..93486212,2	MCF-7	breast:
9	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
10	chr15:93375453..93377764-chr15:93448296..93450344,2	MCF-7	breast:
11	chr15:93282638..93284980-chr15:93448208..93449935,2	MCF-7	breast:
12	chr15:93413469..93415304-chr15:93448158..93450085,2	K562	blood:
13	chr15:93448661..93449558-chr16:74777222..74778009,2	Hela-S3	cervix:
14	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
15	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:
16	chr1:11967066..11969655-chr15:93447237..93449249,2	K562	blood:
17	chr15:93448654..93449226-chr17:41438263..41438994,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000258922	Chromatin interaction
ENSG00000258527	Chromatin interaction
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17648415	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28407548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28458425	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28590319	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62023142	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17704838	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93442600-93449000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:93443200-93449200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:93443200-93449400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:93443200-93449800	Active TSS	Right Ventricle	heart
5	chr15:93443200-93450000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr15:93443200-93450000	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr15:93443400-93449200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr15:93443400-93449800	Active TSS	Psoas Muscle	Psoas
9	chr15:93443400-93450000	Active TSS	Right Atrium	heart
10	chr15:93443600-93449200	Active TSS	Fetal Muscle Leg	muscle
11	chr15:93446200-93450200	Active TSS	Liver	Liver
12	chr15:93446800-93449400	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr15:93446800-93450400	Active TSS	Stomach Smooth Muscle	stomach
14	chr15:93447400-93450000	Active TSS	K562	blood
15	chr15:93447600-93450600	Weak transcription	Spleen	Spleen
16	chr15:93447800-93449000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr15:93447800-93449200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr15:93447800-93449600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr15:93447800-93449600	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr15:93448000-93449000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr15:93448000-93449000	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr15:93448000-93449200	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr15:93448000-93449600	Flanking Active TSS	Osteobl	bone
24	chr15:93448000-93449800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:93448000-93449800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:93448000-93449800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr15:93448000-93449800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr15:93448000-93450800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr15:93448000-93451200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:93448000-93451400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:93448000-93452000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:93448000-93452000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:93448000-93452000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:93448000-93452000	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr15:93448000-93452000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:93448000-93452800	Flanking Active TSS	HUVEC	blood vessel
37	chr15:93448200-93449000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:93448200-93449000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
39	chr15:93448200-93449000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr15:93448200-93449000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr15:93448200-93449000	Flanking Active TSS	Fetal Kidney	kidney
42	chr15:93448200-93449000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr15:93448200-93449200	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr15:93448200-93449200	Flanking Active TSS	Fetal Brain Male	brain
45	chr15:93448200-93449600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr15:93448200-93449800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr15:93448200-93449800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr15:93448200-93449800	Flanking Active TSS	NHEK	skin
49	chr15:93448200-93451200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:93448200-93451200	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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