Variant report

Variant	rs10977104
Chromosome Location	chr9:8437141-8437142
allele	C/G
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: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10481621	0.92[CHB][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10815874	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10815875	0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10977099	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10977101	0.92[ASN][1000 genomes]
rs10977102	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10977103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977105	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10977106	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977108	0.97[ASN][1000 genomes]
rs10977109	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]
rs12551693	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12554079	0.87[ASN][1000 genomes]
rs1323584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323585	0.83[JPT][hapmap]
rs1392521	1.00[YRI][hapmap]
rs2381802	0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs3739577	1.00[YRI][hapmap]
rs7853571	1.00[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7869958	0.94[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs7870456	0.88[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10977104	RLN1	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr9:8402800-8438000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:8405800-8438000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:8418200-8476000	Weak transcription	Fetal Brain Male	brain
6	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:8419800-8447600	Weak transcription	Fetal Brain Female	brain
8	chr9:8420600-8466000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
10	chr9:8421400-8456400	Weak transcription	Ovary	ovary
11	chr9:8422000-8464800	Weak transcription	Brain Germinal Matrix	brain
12	chr9:8423200-8446800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
14	chr9:8424600-8437800	Weak transcription	Fetal Heart	heart
15	chr9:8425600-8447600	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:8428000-8447400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:8430200-8465000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:8431400-8438000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:8431400-8438200	Weak transcription	Brain Angular Gyrus	brain
20	chr9:8432600-8448400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:8432800-8447400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:8433800-8442800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:8434200-8485200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:8436600-8437200	Enhancers	Brain Cingulate Gyrus	brain
25	chr9:8436800-8438200	Enhancers	Brain Substantia Nigra	brain
26	chr9:8436800-8438800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:8436800-8439000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:8436800-8446600	Weak transcription	Fetal Lung	lung
29	chr9:8437000-8437600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr9:8437000-8437800	Enhancers	Brain Hippocampus Middle	brain
31	chr9:8437000-8438400	Enhancers	Placenta Amnion	Placenta Amnion

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