Variant report

Variant	rs4743980
Chromosome Location	chr9:97809853-97809854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr9:97809754-97811539	A549	lung:	n/a	chr9:97810045-97810054 chr9:97810938-97810951 chr9:97810843-97810856 chr9:97810846-97810859 chr9:97810845-97810854 chr9:97810844-97810857 chr9:97810840-97810853
2	MXI1	chr9:97809653-97811945	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97809451..97811509-chr9:97815332..97819190,3	K562	blood:
2	chr9:97809147..97811872-chr9:97817665..97820103,3	MCF-7	breast:
3	chr9:97765581..97769970-chr9:97809027..97814302,8	MCF-7	breast:
4	chr9:97809551..97811519-chr9:97887911..97889998,2	MCF-7	breast:
5	chr9:97804859..97806414-chr9:97808670..97810361,2	MCF-7	breast:
6	chr9:97800986..97803575-chr9:97807961..97810868,3	K562	blood:
7	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
8	chr9:97800135..97801967-chr9:97807867..97810456,2	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1004373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117370	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119512	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121760	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123819	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1020963	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10512253	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761364	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761366	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761368	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10761369	0.82[EUR][1000 genomes]
rs10761372	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10993427	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10993464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993467	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113102	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1412488	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1564234	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1571894	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1571895	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2061800	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404305	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404456	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802454	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3802456	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3858089	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4537362	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743981	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4743982	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744422	0.80[AMR][1000 genomes]
rs4744423	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744424	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744425	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744428	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744430	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744431	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744432	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744435	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744436	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479588	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479591	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479592	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7020709	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021351	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7022452	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7043705	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048786	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851173	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7854831	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7857679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863291	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865144	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7871218	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873479	0.80[AMR][1000 genomes]
rs7873567	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs962229	0.84[AMR][1000 genomes];0.90[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
rs4743980	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
3	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:97799400-97810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:97801600-97810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:97803000-97810800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:97804000-97810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:97804400-97810400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:97804400-97810800	Weak transcription	K562	blood
10	chr9:97805000-97810000	Weak transcription	Brain Anterior Caudate	brain
11	chr9:97805200-97810400	Weak transcription	Brain Angular Gyrus	brain
12	chr9:97805400-97810600	Weak transcription	Small Intestine	intestine
13	chr9:97805600-97810800	Weak transcription	GM12878-XiMat	blood
14	chr9:97806400-97810600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:97806600-97810400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:97807000-97810400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:97807000-97811000	Weak transcription	Stomach Mucosa	stomach
18	chr9:97807200-97810000	Weak transcription	HMEC	breast
19	chr9:97807200-97810000	Weak transcription	HSMMtube	muscle
20	chr9:97807200-97810200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:97807200-97810200	Weak transcription	Hela-S3	cervix
22	chr9:97807200-97810400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:97807400-97810000	Weak transcription	Fetal Lung	lung
24	chr9:97807400-97810800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:97807600-97810400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:97807800-97810000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:97807800-97810400	Weak transcription	Adipose Nuclei	Adipose
28	chr9:97807800-97810800	Weak transcription	Colonic Mucosa	Colon
29	chr9:97808000-97810000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr9:97808000-97810000	Weak transcription	Osteobl	bone
31	chr9:97808000-97810400	Weak transcription	Right Atrium	heart
32	chr9:97808000-97810800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:97808000-97810800	Enhancers	Fetal Heart	heart
34	chr9:97808200-97810000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:97808200-97810200	Weak transcription	Psoas Muscle	Psoas
36	chr9:97808200-97810400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr9:97808200-97810400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
38	chr9:97808200-97810400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr9:97808200-97810400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:97808200-97810400	Weak transcription	NH-A	brain
41	chr9:97808200-97810600	Enhancers	Rectal Smooth Muscle	rectum
42	chr9:97808200-97810600	Weak transcription	Right Ventricle	heart
43	chr9:97808200-97810800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:97808200-97810800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
45	chr9:97808200-97810800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
46	chr9:97808200-97810800	Weak transcription	Lung	lung
47	chr9:97808200-97810800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr9:97808200-97810800	Weak transcription	Spleen	Spleen
49	chr9:97808200-97810800	Weak transcription	NHLF	lung
50	chr9:97808400-97810000	Enhancers	Skeletal Muscle Male	skeletal muscle

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