Variant report

Variant	rs12908494
Chromosome Location	chr15:93462050-93462051
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 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	chr15:93459389..93462852-chr15:93472444..93474181,3	K562	blood:
8	chr15:93350620..93356582-chr15:93455419..93466792,23	MCF-7	breast:
9	chr15:93461235..93463110-chr15:93467839..93470762,2	K562	blood:
10	chr15:93459868..93463900-chr15:93464643..93468863,9	K562	blood:
11	chr15:93339719..93342145-chr15:93460930..93462920,3	MCF-7	breast:
12	chr15:93352539..93354276-chr15:93460171..93462164,2	K562	blood:
13	chr15:93461610..93464401-chr15:93531914..93533700,2	K562	blood:

No data

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

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10520716	0.88[EUR][1000 genomes]
rs11074120	0.86[AMR][1000 genomes]
rs11634566	0.81[EUR][1000 genomes]
rs12437674	0.86[EUR][1000 genomes]
rs12438635	0.80[EUR][1000 genomes]
rs12443243	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594991	0.82[EUR][1000 genomes]
rs1318689	0.90[ASN][1000 genomes]
rs1320819	0.88[EUR][1000 genomes]
rs1406714	0.93[ASN][1000 genomes]
rs1881834	0.83[AMR][1000 genomes]
rs1881835	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28573213	0.94[ASN][1000 genomes]
rs3743469	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3826036	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4327000	0.87[EUR][1000 genomes]
rs6497009	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6497010	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7164668	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167194	0.86[EUR][1000 genomes]
rs7168780	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171151	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7173103	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175134	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8024528	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8026679	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8026695	0.92[ASN][1000 genomes]
rs8035739	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8042395	0.81[AMR][1000 genomes]
rs8042632	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9302362	0.81[AMR][1000 genomes]
rs961233	0.90[ASN][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
rs12908494	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	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:93457200-93464000	Weak transcription	Gastric	stomach
7	chr15:93457800-93464200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:93458200-93463600	Weak transcription	Small Intestine	intestine
9	chr15:93458400-93462200	Weak transcription	Colonic Mucosa	Colon
10	chr15:93458400-93463600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:93459600-93463000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:93459800-93463600	Enhancers	Primary T cells from cord blood	blood
13	chr15:93460000-93462200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:93460000-93462800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:93460000-93464000	Weak transcription	Right Ventricle	heart
16	chr15:93460000-93464200	Weak transcription	Esophagus	oesophagus
17	chr15:93460000-93464200	Weak transcription	Spleen	Spleen
18	chr15:93460400-93462600	Enhancers	Fetal Intestine Large	intestine
19	chr15:93460600-93462600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:93460600-93466400	Genic enhancers	Fetal Intestine Small	intestine
21	chr15:93460800-93462200	Weak transcription	Left Ventricle	heart
22	chr15:93460800-93463600	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:93460800-93464000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr15:93460800-93464000	Weak transcription	Pancreas	Pancrea
25	chr15:93460800-93464200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:93460800-93464400	Weak transcription	Lung	lung
27	chr15:93461000-93462400	Active TSS	Aorta	Aorta
28	chr15:93461000-93463600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:93461000-93464000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:93461200-93462200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:93461200-93462200	Weak transcription	Psoas Muscle	Psoas
32	chr15:93461200-93462400	Enhancers	A549	lung
33	chr15:93461200-93462600	Enhancers	Primary B cells from cord blood	blood
34	chr15:93461200-93462600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:93461200-93462600	Weak transcription	Brain Angular Gyrus	brain
36	chr15:93461200-93462600	Enhancers	Duodenum Mucosa	Duodenum
37	chr15:93461200-93462800	Weak transcription	HMEC	breast
38	chr15:93461200-93462800	Enhancers	HSMM	muscle
39	chr15:93461200-93463000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:93461200-93463600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:93461200-93463800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:93461200-93464000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:93461200-93464000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr15:93461200-93464000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:93461200-93464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:93461200-93464200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:93461200-93464800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr15:93461200-93465600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:93461200-93465600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:93461200-93465800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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