Variant report

Variant	rs16909365
Chromosome Location	chr9:2720701-2720702
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	chr9:2717251..2720244-chr9:2720440..2722938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168263	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1007021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1007022	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs10967100	1.00[CHB][hapmap]
rs12341721	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12343218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12348301	1.00[CHB][hapmap]
rs12352254	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12352612	1.00[EUR][1000 genomes]
rs1355640	1.00[CHB][hapmap]
rs1473839	1.00[CHB][hapmap]
rs1512713	1.00[CHB][hapmap]
rs17656045	1.00[CHB][hapmap]
rs2168136	1.00[CHB][hapmap]
rs41306094	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41312842	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs575205	1.00[CHB][hapmap]
rs60573542	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73390710	0.85[EUR][1000 genomes]
rs73639029	0.91[AMR][1000 genomes]
rs7856406	0.83[EUR][1000 genomes]
rs7858086	1.00[CHB][hapmap]
rs7859924	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864004	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers 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 target site	14 gene(s)	inside rSNPs	diseases
3	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv531565	chr9:2682523-2784028	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv516425	chr9:2690980-2790307	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv892080	chr9:2691186-2721249	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1030063	chr9:2691667-2729595	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1032667	chr9:2691667-2788242	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1019973	chr9:2691812-2790419	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv539935	chr9:2691812-2790419	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv892082	chr9:2699606-2833267	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
15	nsv1021572	chr9:2703159-2790123	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
17	nsv1032100	chr9:2720207-2766110	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2697200-2722800	Weak transcription	HSMM	muscle
2	chr9:2700600-2727800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:2701600-2727800	Weak transcription	Pancreas	Pancrea
4	chr9:2702000-2721400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:2702200-2722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:2702600-2722800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:2710000-2722800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:2710000-2723800	Weak transcription	HSMMtube	muscle
9	chr9:2712000-2722600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:2714800-2727800	Weak transcription	Ovary	ovary
11	chr9:2715600-2722800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:2715800-2727800	Weak transcription	Osteobl	bone
13	chr9:2716200-2729200	Weak transcription	Right Ventricle	heart
14	chr9:2716400-2727800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:2717000-2725400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:2717400-2725200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:2718000-2772800	Weak transcription	Aorta	Aorta
18	chr9:2718200-2722800	Weak transcription	Adipose Nuclei	Adipose
19	chr9:2718400-2722800	Weak transcription	Fetal Lung	lung
20	chr9:2718400-2728200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr9:2718600-2722600	Weak transcription	HMEC	breast
22	chr9:2718600-2722800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:2719000-2721400	Enhancers	HepG2	liver
24	chr9:2719000-2722600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:2719000-2722600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:2719000-2722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:2719000-2722800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:2719000-2722800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:2719000-2725400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:2719000-2726400	Weak transcription	Fetal Brain Male	brain
31	chr9:2719000-2726600	Weak transcription	Esophagus	oesophagus
32	chr9:2719000-2727800	Weak transcription	Gastric	stomach
33	chr9:2719200-2722600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:2719200-2722800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:2719200-2722800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:2719200-2722800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:2719200-2722800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:2719200-2722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:2719200-2722800	Weak transcription	Fetal Muscle Leg	muscle
40	chr9:2719200-2722800	Weak transcription	Fetal Stomach	stomach
41	chr9:2719200-2726600	Weak transcription	NHLF	lung
42	chr9:2719200-2727800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:2719200-2768400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:2719200-2768400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:2719400-2722600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:2719400-2722600	Weak transcription	NHEK	skin
47	chr9:2719600-2720800	Enhancers	Liver	Liver
48	chr9:2719600-2728000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr9:2719800-2722800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:2720000-2727400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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