Variant report

Variant	rs8028865
Chromosome Location	chr15:93461531-93461532
allele	A/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	chr15:93460439..93463062-chr15:93468763..93470874,2	MCF-7	breast:
2	chr15:93339283..93342293-chr15:93459393..93462402,3	MCF-7	breast:
3	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
4	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
5	chr15:93340259..93341092-chr15:93461214..93462175,6	K562	blood:
6	chr15:93360172..93364704-chr15:93459982..93465049,6	MCF-7	breast:
7	chr15:93443429..93444062-chr15:93460752..93461581,2	Hela-S3	cervix:
8	chr15:93459389..93462852-chr15:93472444..93474181,3	K562	blood:
9	chr15:93340168..93341091-chr15:93461034..93461984,5	MCF-7	breast:
10	chr15:93350620..93356582-chr15:93455419..93466792,23	MCF-7	breast:
11	chr15:93352026..93352933-chr15:93460903..93461819,3	MCF-7	breast:
12	chr15:93461235..93463110-chr15:93467839..93470762,2	K562	blood:
13	chr15:93459868..93463900-chr15:93464643..93468863,9	K562	blood:
14	chr15:93339719..93342145-chr15:93460930..93462920,3	MCF-7	breast:
15	chr15:93351934..93352899-chr15:93460819..93461743,4	MCF-7	breast:
16	chr15:93352539..93354276-chr15:93460171..93462164,2	K562	blood:
17	chr15:93352002..93352975-chr15:93460874..93461822,6	K562	blood:

No data

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

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10152428	1.00[CHB][hapmap]
rs11074124	1.00[CHB][hapmap]
rs12900800	1.00[CHB][hapmap]
rs1406712	1.00[CHB][hapmap]
rs1470072	0.90[AMR][1000 genomes]
rs16947284	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525576	0.87[CEU][hapmap]
rs17610095	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs17610312	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17610452	1.00[CHB][hapmap]
rs2272458	1.00[CHB][hapmap]
rs2272463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4778061	1.00[CHB][hapmap]
rs4778064	0.80[AMR][1000 genomes]
rs6497014	1.00[CHB][hapmap]
rs7166161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172853	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173808	0.90[AMR][1000 genomes]
rs7174740	1.00[CHB][hapmap]
rs7180629	1.00[CHB][hapmap]
rs8032603	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes]
rs8041241	0.87[CEU][hapmap];1.00[CHB][hapmap]

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
rs8028865	CHD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93451800-93464000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:93454000-93464000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:93455600-93464400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:93455600-93464800	Weak transcription	Fetal Brain Female	brain
5	chr15:93456600-93461600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:93457200-93464000	Weak transcription	Gastric	stomach
8	chr15:93457800-93464200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:93458200-93461800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:93458200-93463600	Weak transcription	Small Intestine	intestine
11	chr15:93458400-93462200	Weak transcription	Colonic Mucosa	Colon
12	chr15:93458400-93463600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:93458800-93461800	Genic enhancers	HepG2	liver
14	chr15:93459000-93461600	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr15:93459200-93461600	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr15:93459200-93461600	Flanking Active TSS	Hela-S3	cervix
17	chr15:93459600-93463000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:93459800-93463600	Enhancers	Primary T cells from cord blood	blood
19	chr15:93460000-93462200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:93460000-93462800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:93460000-93464000	Weak transcription	Right Ventricle	heart
22	chr15:93460000-93464200	Weak transcription	Esophagus	oesophagus
23	chr15:93460000-93464200	Weak transcription	Spleen	Spleen
24	chr15:93460400-93462600	Enhancers	Fetal Intestine Large	intestine
25	chr15:93460600-93461600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:93460600-93461600	Enhancers	Brain Germinal Matrix	brain
27	chr15:93460600-93461600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr15:93460600-93461800	Enhancers	Primary hematopoietic stem cells	blood
29	chr15:93460600-93462600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:93460600-93466400	Genic enhancers	Fetal Intestine Small	intestine
31	chr15:93460800-93461600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:93460800-93461600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr15:93460800-93461600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr15:93460800-93461600	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr15:93460800-93461600	Active TSS	Right Atrium	heart
36	chr15:93460800-93461600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
37	chr15:93460800-93461600	Flanking Active TSS	HUVEC	blood vessel
38	chr15:93460800-93461600	Transcr. at gene 5' and 3'	K562	blood
39	chr15:93460800-93461600	Flanking Active TSS	NHDF-Ad	bronchial
40	chr15:93460800-93461800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr15:93460800-93461800	Genic enhancers	NH-A	brain
42	chr15:93460800-93462200	Weak transcription	Left Ventricle	heart
43	chr15:93460800-93463600	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:93460800-93464000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr15:93460800-93464000	Weak transcription	Pancreas	Pancrea
46	chr15:93460800-93464200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:93460800-93464400	Weak transcription	Lung	lung
48	chr15:93461000-93461600	Active TSS	Ovary	ovary
49	chr15:93461000-93462400	Active TSS	Aorta	Aorta
50	chr15:93461000-93463600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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