Variant report

Variant	rs10977109
Chromosome Location	chr9:8441203-8441204
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:8435134..8437912-chr9:8440179..8442505,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10481621	0.84[CHB][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10815874	1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs10815875	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs10977099	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10977101	0.84[ASN][1000 genomes]
rs10977102	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10977103	0.89[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10977104	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs10977105	0.94[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs10977106	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10977108	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10977119	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12551693	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12554079	1.00[ASN][1000 genomes]
rs1323584	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1323585	0.88[JPT][hapmap]
rs2381802	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs7853571	1.00[ASW][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7869958	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs7870456	0.82[JPT][hapmap]

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	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv892226	chr9:8435525-8522326	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8389600-8451000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:8402600-8448800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:8418200-8476000	Weak transcription	Fetal Brain Male	brain
4	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:8419800-8447600	Weak transcription	Fetal Brain Female	brain
6	chr9:8420600-8466000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
8	chr9:8421400-8456400	Weak transcription	Ovary	ovary
9	chr9:8422000-8464800	Weak transcription	Brain Germinal Matrix	brain
10	chr9:8423200-8446800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
12	chr9:8425600-8447600	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:8428000-8447400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:8430200-8465000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:8432600-8448400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:8432800-8447400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:8433800-8442800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:8434200-8485200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:8436800-8446600	Weak transcription	Fetal Lung	lung
20	chr9:8437800-8441600	Weak transcription	Brain Hippocampus Middle	brain
21	chr9:8438200-8446800	Weak transcription	Brain Anterior Caudate	brain
22	chr9:8438200-8457600	Weak transcription	Fetal Heart	heart
23	chr9:8438400-8441800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:8438400-8447600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:8438600-8448400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:8438600-8459800	Weak transcription	Brain Angular Gyrus	brain
27	chr9:8439000-8447000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:8439200-8442000	Enhancers	Brain Substantia Nigra	brain
29	chr9:8439600-8447600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:8440400-8442200	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr9:8441000-8447000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:8441200-8441600	Enhancers	Brain Cingulate Gyrus	brain

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