Variant report

Variant	rs12684556
Chromosome Location	chr9:109748077-109748078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:109746997..109749733-chr9:109755308..109756975,2	MCF-7	breast:
2	chr9:109746566..109748897-chr9:109752166..109756916,4	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12003150	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12005883	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12350828	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12685671	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12686587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546484	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs16925955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16925965	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs16926035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16926052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28633093	0.93[ASN][1000 genomes]
rs3764523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs57147563	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57466834	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58231792	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58403995	0.97[ASN][1000 genomes]
rs58419285	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58431218	0.94[ASN][1000 genomes]
rs58984661	0.97[ASN][1000 genomes]
rs60354530	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60858521	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477551	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6477552	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7031901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7043419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs73524922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73524927	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73524936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7848294	1.00[CEU][hapmap]
rs7848891	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7851411	1.00[CEU][hapmap]
rs7860806	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7865611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874076	1.00[CEU][hapmap]
rs9695567	0.84[ASN][1000 genomes]

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:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:109728000-109776200	Weak transcription	NHDF-Ad	bronchial
2	chr9:109729400-109749800	Weak transcription	Pancreas	Pancrea
3	chr9:109729400-109758600	Weak transcription	A549	lung
4	chr9:109733000-109759200	Weak transcription	Fetal Heart	heart
5	chr9:109733200-109775200	Weak transcription	Gastric	stomach
6	chr9:109733600-109759800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:109733800-109749200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:109734000-109751400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:109734000-109751600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:109734000-109752000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:109734000-109752200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:109734000-109752600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:109734200-109749400	Strong transcription	Fetal Intestine Large	intestine
14	chr9:109734200-109751400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:109734200-109751800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:109734200-109768600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:109734400-109748600	Strong transcription	Fetal Lung	lung
18	chr9:109734400-109751400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:109734400-109763000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:109734400-109763200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:109734400-109768800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:109734600-109758000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr9:109734600-109763000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:109734800-109760200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:109734800-109762800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:109736400-109751400	Weak transcription	Small Intestine	intestine
27	chr9:109736800-109777400	Weak transcription	HUVEC	blood vessel
28	chr9:109739400-109764600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:109739600-109768200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr9:109739600-109770000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:109739600-109773000	Weak transcription	Dnd41	blood
32	chr9:109740000-109776000	Weak transcription	Psoas Muscle	Psoas
33	chr9:109740200-109772200	Weak transcription	Colonic Mucosa	Colon
34	chr9:109740200-109777200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:109741200-109749200	Strong transcription	Fetal Muscle Leg	muscle
36	chr9:109741800-109771000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:109742200-109756000	Weak transcription	Colon Smooth Muscle	Colon
38	chr9:109742800-109751600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr9:109743000-109754600	Weak transcription	Spleen	Spleen
40	chr9:109743000-109755800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr9:109743000-109765000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr9:109743200-109753600	Weak transcription	HSMM	muscle
43	chr9:109744000-109751800	Strong transcription	Ovary	ovary
44	chr9:109744400-109748800	Strong transcription	HMEC	breast
45	chr9:109744400-109749200	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr9:109744600-109750800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr9:109744600-109755400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:109745000-109749200	Strong transcription	Adipose Nuclei	Adipose
49	chr9:109745400-109749000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:109745400-109751000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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