Variant report

Variant	rs548824
Chromosome Location	chr9:14088789-14088790
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	chr9:14087200..14091584-chr9:14091633..14096199,6	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10118048	0.83[AFR][1000 genomes]
rs12340320	0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs12348427	0.93[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1689281	0.85[EUR][1000 genomes]
rs2307079	0.81[TSI][hapmap]
rs475732	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs510970	1.00[ASW][hapmap];0.90[LWK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes]
rs551272	0.83[TSI][hapmap]
rs552338	0.82[YRI][hapmap];0.98[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs571693	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs576216	0.80[TSI][hapmap]
rs578720	0.85[EUR][1000 genomes]
rs578809	0.85[EUR][1000 genomes]
rs579735	0.86[EUR][1000 genomes]
rs766402	0.86[AFR][1000 genomes]
rs7858	0.84[ASW][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer 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
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs548824	PPIC	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14073400-14092600	Weak transcription	Aorta	Aorta
2	chr9:14074800-14090400	Weak transcription	Adipose Nuclei	Adipose
3	chr9:14075400-14116000	Weak transcription	Gastric	stomach
4	chr9:14077800-14088800	Weak transcription	Fetal Brain Female	brain
5	chr9:14078000-14112800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:14079800-14094400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:14080000-14095400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:14081400-14096200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:14081400-14096400	Weak transcription	Brain Germinal Matrix	brain
10	chr9:14081400-14115800	Weak transcription	Hela-S3	cervix
11	chr9:14081800-14095600	Weak transcription	Fetal Brain Male	brain
12	chr9:14082000-14090400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:14082000-14096200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:14082000-14096200	Weak transcription	Osteobl	bone
15	chr9:14082200-14096000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:14082200-14096000	Weak transcription	HMEC	breast
17	chr9:14082400-14096400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:14082400-14096600	Weak transcription	Liver	Liver
19	chr9:14082600-14092200	Weak transcription	NH-A	brain
20	chr9:14082600-14096000	Weak transcription	NHEK	skin
21	chr9:14083000-14092200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:14083000-14096200	Weak transcription	Ovary	ovary
23	chr9:14083400-14096200	Weak transcription	Psoas Muscle	Psoas
24	chr9:14083400-14096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:14083800-14096000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:14084200-14089200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:14084400-14090200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:14084800-14098600	Weak transcription	Pancreas	Pancrea
29	chr9:14085000-14094000	Weak transcription	A549	lung
30	chr9:14085200-14092000	Weak transcription	Lung	lung
31	chr9:14085200-14096000	Weak transcription	Right Atrium	heart
32	chr9:14085400-14088800	Strong transcription	Left Ventricle	heart
33	chr9:14085400-14096200	Weak transcription	Right Ventricle	heart
34	chr9:14085800-14088800	Weak transcription	Fetal Heart	heart
35	chr9:14086000-14115600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr9:14086400-14089000	Strong transcription	Fetal Lung	lung
37	chr9:14087400-14089000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:14087400-14092200	Weak transcription	HUVEC	blood vessel
39	chr9:14087800-14088800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:14088000-14088800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:14088000-14092600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr9:14088000-14094000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:14088000-14094800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:14088200-14089400	Genic enhancers	Fetal Muscle Leg	muscle
45	chr9:14088200-14090600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:14088200-14091000	Enhancers	HSMM	muscle
47	chr9:14088200-14096400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr9:14088400-14096200	Weak transcription	Fetal Stomach	stomach
49	chr9:14088600-14089400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr9:14088600-14091000	Enhancers	Muscle Satellite Cultured Cells	--

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