Variant report

Variant	rs10117370
Chromosome Location	chr9:97814524-97814525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:97814309-97814805	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97812899..97815881-chr9:97854427..97857279,2	MCF-7	breast:
2	chr9:97810097..97812414-chr9:97813223..97817126,5	MCF-7	breast:
3	chr9:97684569..97686306-chr9:97814006..97816839,2	MCF-7	breast:
4	chr9:97814331..97816887-chr9:97827066..97829674,2	MCF-7	breast:
5	chr9:97813946..97816396-chr9:97851072..97855306,4	MCF-7	breast:
6	chr9:97812810..97815819-chr9:97816453..97821719,4	K562	blood:
7	chr9:97813367..97817167-chr9:97817537..97820356,4	K562	blood:

No data

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1004373	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119512	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121760	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123819	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1020963	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10512253	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761364	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761366	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761368	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10761372	0.80[ASN][1000 genomes]
rs10993427	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10993464	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993467	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113102	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1412488	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1564234	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1571894	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1571895	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061800	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404305	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404456	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802454	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3802456	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3858089	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4537362	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743979	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743980	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743981	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743982	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743984	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744423	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744424	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744425	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744426	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744428	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744430	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744431	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744432	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744433	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744435	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4744436	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6479588	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6479591	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479592	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7020709	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021351	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7022452	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7043705	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048786	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048941	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851173	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7854831	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7857679	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862156	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863291	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865144	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7871218	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873567	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs962229	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10117370	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97810000-97816800	Transcr. at gene 5' and 3'	A549	lung
2	chr9:97811200-97815200	Weak transcription	Small Intestine	intestine
3	chr9:97811400-97816000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:97811400-97820800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:97811600-97816000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:97811600-97817600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:97811600-97817600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:97811600-97817800	Weak transcription	Right Ventricle	heart
9	chr9:97811800-97815200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:97812000-97816400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:97812400-97817400	Weak transcription	GM12878-XiMat	blood
12	chr9:97812600-97816400	Weak transcription	HUVEC	blood vessel
13	chr9:97812600-97817400	Weak transcription	Adipose Nuclei	Adipose
14	chr9:97812600-97818600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:97812800-97815200	Enhancers	HepG2	liver
16	chr9:97812800-97816400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:97812800-97816400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:97812800-97816800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:97812800-97817600	Weak transcription	Right Atrium	heart
20	chr9:97813000-97814600	Weak transcription	Aorta	Aorta
21	chr9:97813000-97815200	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:97813000-97815200	Weak transcription	Ovary	ovary
23	chr9:97813000-97815200	Weak transcription	Pancreas	Pancrea
24	chr9:97813000-97815200	Weak transcription	Psoas Muscle	Psoas
25	chr9:97813000-97815600	Weak transcription	NH-A	brain
26	chr9:97813000-97816000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:97813000-97816000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:97813000-97816000	Weak transcription	Left Ventricle	heart
29	chr9:97813000-97816200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:97813000-97816200	Weak transcription	Fetal Intestine Large	intestine
31	chr9:97813000-97816400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:97813000-97817800	Weak transcription	Colonic Mucosa	Colon
33	chr9:97813000-97817800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:97813000-97817800	Weak transcription	Lung	lung
35	chr9:97813000-97818200	Weak transcription	Stomach Mucosa	stomach
36	chr9:97813000-97819600	Weak transcription	Hela-S3	cervix
37	chr9:97813000-97820600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:97813000-97873000	Weak transcription	K562	blood
39	chr9:97813200-97815200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:97813200-97815200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:97813200-97815400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:97813200-97815800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr9:97813200-97816000	Strong transcription	Osteobl	bone
44	chr9:97813200-97816400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:97813200-97816400	Weak transcription	HSMMtube	muscle
46	chr9:97813200-97817000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr9:97813200-97817400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:97813200-97817400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr9:97813200-97817600	Weak transcription	Brain Anterior Caudate	brain
50	chr9:97813200-97817600	Weak transcription	Brain Cingulate Gyrus	brain

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