Variant report

Variant	rs9825199
Chromosome Location	chr3:194904584-194904585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194903017..194905147-chr3:194909122..194910993,2	MCF-7	breast:
2	chr3:194884939..194887943-chr3:194901496..194904644,3	K562	blood:
3	chr3:194898020..194901204-chr3:194901654..194905112,7	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11919965	0.91[GIH][hapmap]
rs11925335	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12496868	0.83[EUR][1000 genomes]
rs12497906	0.90[GIH][hapmap]
rs1874102	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1961324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2410805	0.89[EUR][1000 genomes]
rs2410806	0.82[ASW][hapmap];0.82[YRI][hapmap]
rs3796160	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56283237	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59190596	0.98[EUR][1000 genomes]
rs6810043	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs721007	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628353	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs9826142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9856486	0.88[ASW][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs9870185	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9870684	1.00[EUR][1000 genomes]
rs9879463	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
12	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
13	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
14	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194881400-194906000	Weak transcription	Hela-S3	cervix
2	chr3:194884800-194908800	Weak transcription	Thymus	Thymus
3	chr3:194885400-194906600	Weak transcription	Gastric	stomach
4	chr3:194892400-194907400	Weak transcription	HSMMtube	muscle
5	chr3:194892600-194906200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:194896600-194908000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:194896600-194909200	Weak transcription	Pancreas	Pancrea
8	chr3:194897000-194906000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:194898800-194905000	Enhancers	Fetal Muscle Leg	muscle
10	chr3:194899400-194905400	Weak transcription	Stomach Mucosa	stomach
11	chr3:194899600-194905600	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:194900200-194906000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:194901200-194905800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:194901200-194908600	Weak transcription	Fetal Heart	heart
15	chr3:194901600-194906200	Weak transcription	Primary B cells from cord blood	blood
16	chr3:194901600-194909000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:194901800-194905000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:194901800-194905600	Weak transcription	Lung	lung
19	chr3:194901800-194905600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr3:194901800-194906800	Weak transcription	HepG2	liver
21	chr3:194902000-194906000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:194902200-194904600	Enhancers	NHLF	lung
23	chr3:194902200-194904800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:194902200-194906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:194902200-194906600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:194902400-194904600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr3:194902400-194904600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:194902400-194904800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr3:194902400-194905000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:194902400-194905000	Enhancers	NHDF-Ad	bronchial
31	chr3:194902400-194906800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:194902600-194904600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:194902600-194904600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:194902600-194904600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:194902600-194904600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:194902600-194904800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr3:194902600-194905000	Enhancers	Fetal Stomach	stomach
38	chr3:194902800-194904600	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:194902800-194904800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:194902800-194905000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:194902800-194905000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr3:194902800-194906200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr3:194903000-194906400	Weak transcription	Spleen	Spleen
44	chr3:194903000-194907400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:194903000-194909000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:194903000-194909000	Weak transcription	Ovary	ovary
47	chr3:194903000-194915200	Weak transcription	Brain Substantia Nigra	brain
48	chr3:194903200-194904800	Enhancers	H9 Cell Line	embryonic stem cell
49	chr3:194903200-194906200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:194903200-194906800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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