Variant report

Variant	rs1411662
Chromosome Location	chr9:85104372-85104373
allele	A/G
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	FOS	chr9:85104159-85105519	MCF10A-Er-Src	breast:	n/a	chr9:85104201-85104213
2	EP300	chr9:85103230-85104556	SK-N-SH_RA	brain:	n/a	n/a
3	FOS	chr9:85104295-85105516	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF263	chr9:85103898-85105579	HEK293-T-REx	kidney:	n/a	n/a
5	KAP1	chr9:85103299-85105594	HEK293	kidney:	n/a	chr9:85103955-85103963
6	ESR1	chr9:85103413-85104452	ECC-1	luminal epithelium:	n/a	n/a
7	ESR1	chr9:85103501-85104464	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr9:85103685-85104453	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr9:85104326-85105475	MCF10A-Er-Src	breast:	n/a	n/a
10	NFIC	chr9:85103622-85104381	ECC-1	luminal epithelium:	n/a	n/a
11	ESR1	chr9:85103603-85104382	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr9:85103740-85105469	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr9:85104247-85105419	MCF10A-Er-Src	breast:	n/a	n/a
14	ESR1	chr9:85103870-85104383	ECC-1	luminal epithelium:	n/a	n/a
15	RAD21	chr9:85104214-85104466	SK-N-SH_RA	brain:	n/a	n/a
16	EP300	chr9:85104059-85104530	SK-N-SH_RA	brain:	n/a	n/a
17	NFIC	chr9:85103660-85104387	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000228430	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10125999	0.84[CEU][hapmap]
rs1041392	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11139569	0.96[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11139570	0.92[ASN][1000 genomes]
rs12350753	0.88[ASN][1000 genomes]
rs12553129	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12683121	0.91[ASN][1000 genomes]
rs12683715	0.91[ASN][1000 genomes]
rs12684844	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12685162	0.91[ASN][1000 genomes]
rs13298628	0.99[ASN][1000 genomes]
rs13299917	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1330817	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1411660	0.91[ASN][1000 genomes]
rs1411661	0.84[ASN][1000 genomes]
rs17085530	0.91[ASN][1000 genomes]
rs17085531	0.91[ASN][1000 genomes]
rs2026194	0.92[ASN][1000 genomes]
rs2889949	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs34637520	0.92[ASN][1000 genomes]
rs34845422	0.84[ASN][1000 genomes]
rs34867546	0.84[ASN][1000 genomes]
rs35089927	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35501117	0.88[ASN][1000 genomes]
rs35576282	0.91[ASN][1000 genomes]
rs35677430	0.91[ASN][1000 genomes]
rs3892417	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4478643	0.80[ASN][1000 genomes]
rs4877232	0.92[ASN][1000 genomes]
rs4877233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877692	0.92[ASN][1000 genomes]
rs4877693	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56291243	0.91[ASN][1000 genomes]
rs67968529	0.91[ASN][1000 genomes]
rs7018522	0.96[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7021813	0.91[ASN][1000 genomes]
rs7036901	0.91[ASN][1000 genomes]
rs7037151	0.91[ASN][1000 genomes]
rs7046852	0.92[ASN][1000 genomes]
rs7850032	0.84[ASN][1000 genomes]
rs7850751	0.89[ASN][1000 genomes]
rs7854052	0.95[CHB][hapmap]
rs7865259	0.84[ASN][1000 genomes]
rs7865649	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893510	chr9:84954592-85117420	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85102200-85105800	Enhancers	Fetal Lung	lung
2	chr9:85102800-85105000	Enhancers	Liver	Liver
3	chr9:85102800-85105000	Enhancers	Brain Anterior Caudate	brain
4	chr9:85102800-85105200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr9:85102800-85105200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr9:85102800-85105200	Enhancers	HepG2	liver
7	chr9:85102800-85105400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:85102800-85105400	Enhancers	Brain Germinal Matrix	brain
9	chr9:85102800-85105600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:85102800-85105600	Enhancers	Fetal Kidney	kidney
11	chr9:85102800-85105800	Enhancers	Adipose Nuclei	Adipose
12	chr9:85102800-85105800	Enhancers	Fetal Muscle Leg	muscle
13	chr9:85102800-85106200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:85103000-85107000	Enhancers	Osteobl	bone
15	chr9:85103200-85105000	Enhancers	Brain Hippocampus Middle	brain
16	chr9:85103200-85105000	Enhancers	NHDF-Ad	bronchial
17	chr9:85103200-85105200	Enhancers	Brain Angular Gyrus	brain
18	chr9:85103200-85105200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr9:85103200-85105600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:85103200-85105600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr9:85103200-85105600	Enhancers	Fetal Stomach	stomach
22	chr9:85103200-85105600	Enhancers	NH-A	brain
23	chr9:85103200-85106000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:85103400-85104400	Enhancers	Brain Substantia Nigra	brain
25	chr9:85103400-85105000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:85103400-85105200	Enhancers	Colon Smooth Muscle	Colon
27	chr9:85103400-85105400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:85103400-85105800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:85103400-85105800	Enhancers	Pancreas	Pancrea
30	chr9:85103600-85104400	Weak transcription	Aorta	Aorta
31	chr9:85103600-85104400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:85103600-85104600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:85103600-85104600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:85103600-85105000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:85103600-85105000	Weak transcription	Right Atrium	heart
36	chr9:85103800-85104600	Enhancers	Primary hematopoietic stem cells	blood
37	chr9:85103800-85105000	Weak transcription	Stomach Mucosa	stomach
38	chr9:85103800-85105000	Flanking Active TSS	HMEC	breast
39	chr9:85103800-85105200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:85103800-85105200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:85103800-85105200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr9:85103800-85109400	Weak transcription	NHLF	lung
43	chr9:85104000-85104400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:85104000-85104400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:85104000-85104800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:85104000-85105000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr9:85104000-85105000	Flanking Active TSS	NHEK	skin
48	chr9:85104000-85105200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:85104000-85105200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:85104200-85104600	Weak transcription	Psoas Muscle	Psoas

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