Variant report

Variant	rs505668
Chromosome Location	chr9:116382381-116382382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116172702..116174409-chr9:116381360..116383255,2	MCF-7	breast:
2	chr9:116382263..116386126-chr9:116386783..116389124,3	MCF-7	breast:
3	chr9:116376628..116378313-chr9:116382222..116384609,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGS3-1	chr9:116382056-116384914	ENSG00000233817

Variant related genes	Relation type
ENSG00000157653	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1547694	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475129	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479766	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483284	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs485184	0.92[AFR][1000 genomes]
rs502942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512779	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530456	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs569679	0.96[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586265	0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs608290	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs632629	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637175	0.96[CEU][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664850	0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs666216	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680929	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
6	nsv466509	chr9:116356516-116396098	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv615216	chr9:116356516-116396098	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv466510	chr9:116363877-116397397	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv615217	chr9:116363877-116397397	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv615218	chr9:116365126-116391069	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv466511	chr9:116374990-116397397	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv615219	chr9:116374990-116397397	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv893749	chr9:116378759-116439749	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116373600-116382400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:116375600-116382400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:116376200-116386000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:116377000-116382800	Enhancers	Primary B cells from peripheral blood	blood
5	chr9:116377400-116382400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:116377800-116382400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:116378000-116382400	Weak transcription	Brain Angular Gyrus	brain
8	chr9:116378600-116382600	Weak transcription	Psoas Muscle	Psoas
9	chr9:116378800-116382400	Weak transcription	Esophagus	oesophagus
10	chr9:116379000-116382400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:116379000-116382600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:116379400-116383000	Weak transcription	Brain Substantia Nigra	brain
13	chr9:116380000-116382400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:116380200-116382400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:116380200-116382400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:116380200-116382600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:116380200-116382800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:116380600-116382600	Enhancers	Fetal Muscle Trunk	muscle
19	chr9:116380600-116384200	Enhancers	Spleen	Spleen
20	chr9:116381000-116382600	Enhancers	Adipose Nuclei	Adipose
21	chr9:116381200-116382400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:116381200-116382400	Enhancers	NHDF-Ad	bronchial
23	chr9:116381200-116382600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr9:116381200-116382600	Enhancers	Stomach Smooth Muscle	stomach
25	chr9:116381200-116384200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:116381200-116384200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:116381200-116384200	Enhancers	Fetal Brain Female	brain
28	chr9:116381200-116385800	Enhancers	Stomach Mucosa	stomach
29	chr9:116381200-116386000	Enhancers	Fetal Muscle Leg	muscle
30	chr9:116381400-116382400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:116381400-116382400	Enhancers	Pancreas	Pancrea
32	chr9:116381400-116382400	Enhancers	NH-A	brain
33	chr9:116381400-116382600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr9:116381400-116383600	Enhancers	Lung	lung
35	chr9:116381400-116384200	Enhancers	Right Ventricle	heart
36	chr9:116381400-116384400	Enhancers	Fetal Brain Male	brain
37	chr9:116381400-116384400	Enhancers	Placenta	Placenta
38	chr9:116381400-116384400	Enhancers	Fetal Stomach	stomach
39	chr9:116381600-116383600	Enhancers	Duodenum Mucosa	Duodenum
40	chr9:116381600-116384200	Enhancers	Brain Germinal Matrix	brain
41	chr9:116381600-116384400	Enhancers	Small Intestine	intestine
42	chr9:116381600-116386000	Enhancers	Fetal Intestine Small	intestine
43	chr9:116381800-116382400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:116381800-116382400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr9:116381800-116382400	Enhancers	HMEC	breast
46	chr9:116381800-116382600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:116381800-116382600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr9:116381800-116382600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr9:116381800-116382600	Enhancers	HSMMtube	muscle
50	chr9:116381800-116382800	Enhancers	Primary hematopoietic stem cells	blood

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