Variant report

Variant	rs12346476
Chromosome Location	chr9:116383326-116383327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116382263..116386126-chr9:116386783..116389124,3	MCF-7	breast:
2	chr9:116383167..116386391-chr9:116389906..116398638,8	MCF-7	breast:
3	chr9:116362421..116364215-chr9:116382528..116385259,2	MCF-7	breast:
4	chr9:116382976..116384778-chr9:116398456..116400066,2	MCF-7	breast:
5	chr9:116376628..116378313-chr9:116382222..116384609,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

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

No data

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs16908653	1.00[EUR][1000 genomes]
rs16909502	1.00[EUR][1000 genomes]
rs6478021	1.00[EUR][1000 genomes]
rs7023224	1.00[EUR][1000 genomes]
rs7027261	1.00[EUR][1000 genomes]
rs7032245	1.00[EUR][1000 genomes]
rs7032414	1.00[EUR][1000 genomes]
rs7033489	1.00[EUR][1000 genomes]
rs7038258	1.00[EUR][1000 genomes]
rs7042609	1.00[EUR][1000 genomes]
rs73538901	1.00[EUR][1000 genomes]
rs73544687	1.00[EUR][1000 genomes]
rs73544688	1.00[EUR][1000 genomes]
rs73548441	1.00[EUR][1000 genomes]
rs73655894	1.00[EUR][1000 genomes]
rs7851265	1.00[EUR][1000 genomes]
rs7853612	1.00[EUR][1000 genomes]
rs7856713	1.00[EUR][1000 genomes]
rs7864169	1.00[EUR][1000 genomes]
rs7865642	1.00[EUR][1000 genomes]
rs7866866	1.00[EUR][1000 genomes]
rs7870008	1.00[EUR][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:102 , 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	chr9:116380600-116384200	Enhancers	Spleen	Spleen
3	chr9:116381200-116384200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:116381200-116384200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:116381200-116384200	Enhancers	Fetal Brain Female	brain
6	chr9:116381200-116385800	Enhancers	Stomach Mucosa	stomach
7	chr9:116381200-116386000	Enhancers	Fetal Muscle Leg	muscle
8	chr9:116381400-116383600	Enhancers	Lung	lung
9	chr9:116381400-116384200	Enhancers	Right Ventricle	heart
10	chr9:116381400-116384400	Enhancers	Fetal Brain Male	brain
11	chr9:116381400-116384400	Enhancers	Placenta	Placenta
12	chr9:116381400-116384400	Enhancers	Fetal Stomach	stomach
13	chr9:116381600-116383600	Enhancers	Duodenum Mucosa	Duodenum
14	chr9:116381600-116384200	Enhancers	Brain Germinal Matrix	brain
15	chr9:116381600-116384400	Enhancers	Small Intestine	intestine
16	chr9:116381600-116386000	Enhancers	Fetal Intestine Small	intestine
17	chr9:116381800-116383600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:116381800-116383600	Enhancers	Colonic Mucosa	Colon
19	chr9:116381800-116384200	Enhancers	Fetal Kidney	kidney
20	chr9:116381800-116384200	Flanking Active TSS	HUVEC	blood vessel
21	chr9:116381800-116386000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:116381800-116386000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:116381800-116386600	Enhancers	NHLF	lung
24	chr9:116381800-116387200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:116382000-116383400	Enhancers	Liver	Liver
26	chr9:116382000-116383400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr9:116382000-116383800	Enhancers	Right Atrium	heart
28	chr9:116382000-116384200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr9:116382000-116384200	Enhancers	Left Ventricle	heart
30	chr9:116382000-116384400	Enhancers	Brain Anterior Caudate	brain
31	chr9:116382000-116384800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:116382000-116386600	Enhancers	Fetal Intestine Large	intestine
33	chr9:116382200-116383400	Bivalent Enhancer	Fetal Thymus	thymus
34	chr9:116382200-116383600	Enhancers	Aorta	Aorta
35	chr9:116382200-116383600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr9:116382200-116383800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr9:116382200-116383800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:116382200-116383800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:116382200-116383800	Flanking Active TSS	Osteobl	bone
40	chr9:116382200-116384200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:116382200-116384200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:116382200-116384200	Enhancers	Brain Hippocampus Middle	brain
43	chr9:116382200-116384400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:116382200-116384400	Enhancers	Fetal Lung	lung
45	chr9:116382200-116384400	Enhancers	Ovary	ovary
46	chr9:116382200-116384800	Weak transcription	Primary B cells from cord blood	blood
47	chr9:116382200-116385600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:116382200-116385800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr9:116382200-116386000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr9:116382200-116386200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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