Variant report

Variant	rs16925955
Chromosome Location	chr9:109703198-109703199
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	chr9:109624590..109626790-chr9:109701721..109704074,2	MCF-7	breast:
2	chr9:109701661..109703680-chr9:109703872..109706134,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148143	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12003150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12005883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12350828	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12684556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12685671	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12686587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1546484	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs16925965	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16926035	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs16926052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2417761	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs28633093	0.93[ASN][1000 genomes]
rs3764523	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs57147563	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57466834	0.95[ASN][1000 genomes]
rs58231792	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58403995	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58419285	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58431218	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58984661	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60354530	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60858521	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6477551	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6477552	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7031901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7039109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7043419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73524922	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73524927	0.93[ASN][1000 genomes]
rs73524936	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7847708	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7848294	1.00[CEU][hapmap]
rs7848891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7851411	1.00[CEU][hapmap]
rs7860806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7865611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7874076	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869202	chr9:108940763-109811530	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv831680	chr9:109653596-109848827	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:109684400-109708000	Weak transcription	Fetal Thymus	thymus
2	chr9:109684800-109705800	Weak transcription	Stomach Mucosa	stomach
3	chr9:109685000-109713000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:109685400-109706600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:109685400-109708600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:109685600-109705200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:109685600-109706600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:109686200-109722600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:109688600-109738600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:109690400-109728600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:109692000-109734200	Weak transcription	Colonic Mucosa	Colon
12	chr9:109692200-109704200	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:109692200-109712200	Weak transcription	Gastric	stomach
14	chr9:109692400-109705800	Strong transcription	Fetal Brain Female	brain
15	chr9:109692600-109705000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:109693200-109705000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:109693200-109711600	Weak transcription	Spleen	Spleen
18	chr9:109695000-109715400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:109696400-109709200	Weak transcription	A549	lung
20	chr9:109697200-109703600	Strong transcription	NHLF	lung
21	chr9:109697600-109711600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:109697800-109706000	Strong transcription	NHEK	skin
23	chr9:109697800-109706200	Strong transcription	Adipose Nuclei	Adipose
24	chr9:109698000-109710600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr9:109698000-109710600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:109698000-109712600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:109698000-109721400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:109698000-109721600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:109698000-109722400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:109698600-109714000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:109698800-109707800	Weak transcription	HUVEC	blood vessel
32	chr9:109698800-109708000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:109699200-109707600	Weak transcription	NHDF-Ad	bronchial
34	chr9:109699200-109709200	Weak transcription	Psoas Muscle	Psoas
35	chr9:109699200-109719000	Weak transcription	Pancreas	Pancrea
36	chr9:109699400-109704000	Weak transcription	Fetal Intestine Small	intestine
37	chr9:109699400-109708000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr9:109699400-109709400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:109700200-109703600	Strong transcription	HSMM	muscle
40	chr9:109700400-109704600	Strong transcription	Fetal Kidney	kidney
41	chr9:109700600-109703600	Strong transcription	Brain Germinal Matrix	brain
42	chr9:109700600-109704600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr9:109700600-109704800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:109700600-109706200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:109700800-109703200	Strong transcription	Colon Smooth Muscle	Colon
46	chr9:109700800-109703400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:109700800-109703800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:109700800-109703800	Strong transcription	Fetal Muscle Leg	muscle
49	chr9:109700800-109705000	Strong transcription	HSMMtube	muscle
50	chr9:109700800-109705200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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