Variant report

Variant	rs502942
Chromosome Location	chr9:116382688-116382689
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	chr9:116362421..116364215-chr9:116382528..116385259,2	MCF-7	breast:
4	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
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1547694	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	0.91[AFR][1000 genomes]
rs485184	0.92[AFR][1000 genomes]
rs505668	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	0.95[AFR][1000 genomes]
rs569679	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586265	0.93[AFR][1000 genomes]
rs608290	0.86[AFR][1000 genomes]
rs632629	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637175	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664850	0.94[AFR][1000 genomes]
rs666216	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116376200-116386000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr9:116377000-116382800	Enhancers	Primary B cells from peripheral blood	blood
3	chr9:116379400-116383000	Weak transcription	Brain Substantia Nigra	brain
4	chr9:116380200-116382800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:116380600-116384200	Enhancers	Spleen	Spleen
6	chr9:116381200-116384200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:116381200-116384200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:116381200-116384200	Enhancers	Fetal Brain Female	brain
9	chr9:116381200-116385800	Enhancers	Stomach Mucosa	stomach
10	chr9:116381200-116386000	Enhancers	Fetal Muscle Leg	muscle
11	chr9:116381400-116383600	Enhancers	Lung	lung
12	chr9:116381400-116384200	Enhancers	Right Ventricle	heart
13	chr9:116381400-116384400	Enhancers	Fetal Brain Male	brain
14	chr9:116381400-116384400	Enhancers	Placenta	Placenta
15	chr9:116381400-116384400	Enhancers	Fetal Stomach	stomach
16	chr9:116381600-116383600	Enhancers	Duodenum Mucosa	Duodenum
17	chr9:116381600-116384200	Enhancers	Brain Germinal Matrix	brain
18	chr9:116381600-116384400	Enhancers	Small Intestine	intestine
19	chr9:116381600-116386000	Enhancers	Fetal Intestine Small	intestine
20	chr9:116381800-116382800	Enhancers	Primary hematopoietic stem cells	blood
21	chr9:116381800-116383600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:116381800-116383600	Enhancers	Colonic Mucosa	Colon
23	chr9:116381800-116384200	Enhancers	Fetal Kidney	kidney
24	chr9:116381800-116384200	Flanking Active TSS	HUVEC	blood vessel
25	chr9:116381800-116386000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:116381800-116386000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:116381800-116386600	Enhancers	NHLF	lung
28	chr9:116381800-116387200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:116382000-116382800	Enhancers	A549	lung
30	chr9:116382000-116383000	Flanking Active TSS	Fetal Heart	heart
31	chr9:116382000-116383000	Weak transcription	GM12878-XiMat	blood
32	chr9:116382000-116383400	Enhancers	Liver	Liver
33	chr9:116382000-116383400	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr9:116382000-116383800	Enhancers	Right Atrium	heart
35	chr9:116382000-116384200	Enhancers	H9 Cell Line	embryonic stem cell
36	chr9:116382000-116384200	Enhancers	Left Ventricle	heart
37	chr9:116382000-116384400	Enhancers	Brain Anterior Caudate	brain
38	chr9:116382000-116384800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:116382000-116386600	Enhancers	Fetal Intestine Large	intestine
40	chr9:116382200-116382800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr9:116382200-116382800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:116382200-116382800	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr9:116382200-116383000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr9:116382200-116383000	Weak transcription	Gastric	stomach
45	chr9:116382200-116383200	Flanking Active TSS	HSMM	muscle
46	chr9:116382200-116383400	Bivalent Enhancer	Fetal Thymus	thymus
47	chr9:116382200-116383600	Enhancers	Aorta	Aorta
48	chr9:116382200-116383600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr9:116382200-116383800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:116382200-116383800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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