Variant report

Variant	rs9988453
Chromosome Location	chr1:155529009-155529010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155520429..155523505-chr1:155527684..155531607,4	K562	blood:
2	chr1:155526189..155529069-chr1:155532173..155534507,2	K562	blood:

Variant related genes	Relation type
ENSG00000116539	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10158037	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10158433	1.00[ASW][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12096547	1.00[CHB][hapmap]
rs13375379	1.00[ASW][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16836851	0.88[ASW][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16836867	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16836868	0.88[ASW][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs2362361	1.00[CHB][hapmap]
rs28438500	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28452675	0.80[AFR][1000 genomes]
rs28491466	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28507559	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56035547	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56770523	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57334798	0.96[AFR][1000 genomes]
rs57519519	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57807227	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58086206	0.85[AFR][1000 genomes]
rs58621120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58850753	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59633238	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59815288	1.00[AMR][1000 genomes]
rs59913551	0.94[AFR][1000 genomes]
rs59992966	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60568057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60818259	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61403978	0.91[AFR][1000 genomes]
rs61631408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs621181	1.00[CHB][hapmap]
rs6427277	0.86[AFR][1000 genomes]
rs6658401	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6659913	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs6665660	1.00[ASW][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6665939	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6669216	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6692952	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72993428	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72993486	0.85[AFR][1000 genomes]
rs72995115	0.88[AFR][1000 genomes]
rs72995140	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995165	0.89[AFR][1000 genomes]
rs72995166	0.93[AFR][1000 genomes]
rs72995171	0.97[AFR][1000 genomes]
rs72995173	0.93[AFR][1000 genomes]
rs72995177	1.00[AFR][1000 genomes]
rs73008931	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008968	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008999	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010906	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010909	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010921	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7517139	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7517777	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7532714	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7541017	0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7549653	0.83[AFR][1000 genomes]
rs9988540	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv872468	chr1:155413304-155549562	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155489800-155529400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:155496600-155529800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:155506400-155529400	Weak transcription	Osteobl	bone
4	chr1:155506400-155529600	Weak transcription	Fetal Lung	lung
5	chr1:155507000-155530200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:155510600-155530200	Weak transcription	Right Ventricle	heart
7	chr1:155511000-155529200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:155511000-155529400	Weak transcription	HepG2	liver
9	chr1:155511400-155529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:155514000-155529400	Weak transcription	Hela-S3	cervix
11	chr1:155514400-155530200	Weak transcription	Pancreas	Pancrea
12	chr1:155514400-155530200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:155514400-155530200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:155516000-155530200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:155516800-155529600	Weak transcription	NHDF-Ad	bronchial
16	chr1:155517000-155531400	Weak transcription	Esophagus	oesophagus
17	chr1:155517400-155529600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:155517600-155530200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:155518200-155529400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:155518200-155531600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:155518600-155530000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:155518600-155531400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:155518800-155529400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:155518800-155529600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:155518800-155530000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:155518800-155530200	Weak transcription	Brain Substantia Nigra	brain
27	chr1:155518800-155530200	Weak transcription	HMEC	breast
28	chr1:155519200-155529400	Weak transcription	NHEK	skin
29	chr1:155519200-155529600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:155519200-155529800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:155519200-155530000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:155520200-155530200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:155522200-155531400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:155522600-155529400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:155522600-155529400	Weak transcription	Brain Germinal Matrix	brain
36	chr1:155523400-155530200	Weak transcription	Fetal Kidney	kidney
37	chr1:155523600-155530000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:155523800-155530200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:155524000-155529400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:155524000-155529600	Weak transcription	Brain Angular Gyrus	brain
41	chr1:155524000-155529600	Weak transcription	Brain Anterior Caudate	brain
42	chr1:155524000-155530000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:155524000-155530200	Weak transcription	NHLF	lung
44	chr1:155524800-155530000	Weak transcription	A549	lung
45	chr1:155524800-155530200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:155525000-155529400	Weak transcription	Stomach Mucosa	stomach
47	chr1:155525200-155530000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:155525600-155530000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:155525600-155530000	Weak transcription	Primary B cells from cord blood	blood
50	chr1:155525800-155529600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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