Variant report

Variant	rs555168817
Chromosome Location	chr9:2292308-2292309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:2292225..2294051-chr9:2294141..2297013,2	MCF-7	breast:
2	chr9:2256748..2259220-chr9:2292192..2293911,2	MCF-7	breast:
3	chr9:2291871..2293597-chr9:2622079..2623974,2	MCF-7	breast:
4	chr9:2290959..2293717-chr9:2295989..2299437,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMARCA2-6	chr9:2291976-2293037	NONHSAT129989

Variant related genes	Relation type
ENSG00000236404	Chromatin interaction
ENSG00000147852	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	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
5	nsv1033628	chr9:2215179-2303623	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv539927	chr9:2215179-2303623	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1029947	chr9:2233969-2364269	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1015332	chr9:2235123-2361722	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1022726	chr9:2235500-2361890	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv539928	chr9:2235500-2361890	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1033537	chr9:2235700-2361750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv539929	chr9:2235700-2361750	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv613127	chr9:2237390-2363874	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv869882	chr9:2249223-2357827	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv613128	chr9:2253678-2419538	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1016677	chr9:2253741-2415423	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1016401	chr9:2255397-2410590	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv613129	chr9:2256092-2330907	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
22	nsv1019572	chr9:2273780-2349950	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	esv2761291	chr9:2281999-2298146	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1020742	chr9:2281999-2298146	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv892062	chr9:2291635-2330643	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv892063	chr9:2291635-2419538	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2286000-2295400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:2286800-2293600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:2287000-2293600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:2287200-2294000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:2288000-2298800	Weak transcription	Pancreas	Pancrea
6	chr9:2288600-2296400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:2289400-2292600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:2289400-2293600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:2289600-2298800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr9:2290400-2292800	Enhancers	Fetal Muscle Leg	muscle
11	chr9:2290800-2295600	Weak transcription	Esophagus	oesophagus
12	chr9:2291200-2292800	Enhancers	Psoas Muscle	Psoas
13	chr9:2291200-2293600	Enhancers	Placenta	Placenta
14	chr9:2291600-2292400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:2291600-2292400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:2291600-2292800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr9:2291600-2292800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr9:2291600-2293600	Enhancers	HSMMtube	muscle
19	chr9:2291800-2292400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:2291800-2292400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:2291800-2292400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:2291800-2292800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:2291800-2292800	Enhancers	NHEK	skin
24	chr9:2291800-2293000	Enhancers	HMEC	breast
25	chr9:2291800-2293600	Enhancers	Stomach Mucosa	stomach
26	chr9:2292000-2292400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr9:2292000-2292400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:2292000-2292400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:2292000-2292400	Enhancers	Brain Germinal Matrix	brain
30	chr9:2292000-2292400	Enhancers	Fetal Intestine Large	intestine
31	chr9:2292000-2292600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:2292000-2292800	Enhancers	Fetal Intestine Small	intestine
33	chr9:2292000-2292800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr9:2292000-2292800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr9:2292000-2293000	Enhancers	Fetal Lung	lung
36	chr9:2292000-2293000	Enhancers	HSMM	muscle
37	chr9:2292000-2293600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:2292200-2292400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr9:2292200-2292600	Enhancers	Rectal Mucosa Donor 29	rectum

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