Variant report

Variant	rs16908998
Chromosome Location	chr9:96054759-96054760
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	chr9:96050880..96053674-chr9:96053740..96056815,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12552078	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12554664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16909009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298244	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34406556	0.87[ASN][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	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96027200-96056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:96031400-96055000	Weak transcription	Colonic Mucosa	Colon
4	chr9:96031400-96062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:96033000-96055000	Weak transcription	Brain Anterior Caudate	brain
6	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
7	chr9:96033400-96062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:96033600-96060200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:96033600-96061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:96033800-96060400	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:96041600-96056800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:96047200-96065000	Weak transcription	Fetal Brain Male	brain
16	chr9:96048200-96057200	Weak transcription	Right Atrium	heart
17	chr9:96049200-96057600	Strong transcription	Fetal Brain Female	brain
18	chr9:96049400-96057000	Strong transcription	Brain Germinal Matrix	brain
19	chr9:96049600-96054800	Enhancers	Fetal Thymus	thymus
20	chr9:96050000-96056600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:96050200-96056800	Strong transcription	Fetal Intestine Small	intestine
22	chr9:96051000-96056600	Weak transcription	Left Ventricle	heart
23	chr9:96051200-96056200	Weak transcription	Fetal Heart	heart
24	chr9:96051400-96056400	Weak transcription	Spleen	Spleen
25	chr9:96051400-96067800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:96051800-96055600	Strong transcription	Pancreas	Pancrea
27	chr9:96052000-96056800	Strong transcription	Fetal Intestine Large	intestine
28	chr9:96052000-96060800	Weak transcription	Placenta	Placenta
29	chr9:96052200-96056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:96052200-96066600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:96052400-96057400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr9:96052800-96056200	Weak transcription	HepG2	liver
33	chr9:96054400-96054800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:96054400-96054800	Weak transcription	Right Ventricle	heart
35	chr9:96054400-96058200	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:96054600-96055200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:96054600-96055400	Strong transcription	Gastric	stomach
38	chr9:96054600-96055400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:96054600-96055600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr9:96054600-96055600	Strong transcription	Fetal Stomach	stomach
41	chr9:96054600-96055600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr9:96054600-96056000	Strong transcription	Rectal Smooth Muscle	rectum
43	chr9:96054600-96056200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:96054600-96056400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr9:96054600-96056400	Weak transcription	Thymus	Thymus
46	chr9:96054600-96056800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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