Variant report

Variant	rs12375674
Chromosome Location	chr9:8452953-8452954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10739164	0.86[AFR][1000 genomes]
rs10739165	0.84[AFR][1000 genomes]
rs10815878	0.86[JPT][hapmap]
rs12375663	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323588	1.00[LWK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs7031287	0.97[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv892227	chr9:8445066-8461714	Enhancers Weak transcription Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases
6	nsv613288	chr9:8447732-8454566	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	inside rSNPs	diseases
7	nsv527205	chr9:8452899-8452953	Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8418200-8476000	Weak transcription	Fetal Brain Male	brain
2	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:8420600-8466000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
5	chr9:8421400-8456400	Weak transcription	Ovary	ovary
6	chr9:8422000-8464800	Weak transcription	Brain Germinal Matrix	brain
7	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
8	chr9:8430200-8465000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr9:8434200-8485200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:8438200-8457600	Weak transcription	Fetal Heart	heart
11	chr9:8438600-8459800	Weak transcription	Brain Angular Gyrus	brain
12	chr9:8442000-8458000	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:8442200-8522200	Weak transcription	Liver	Liver
14	chr9:8447200-8456200	Weak transcription	Brain Anterior Caudate	brain
15	chr9:8447800-8468200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:8448000-8468200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:8448000-8494800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:8448200-8456000	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:8448400-8472800	Weak transcription	Fetal Stomach	stomach
20	chr9:8449000-8454600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:8449000-8465000	Weak transcription	Fetal Brain Female	brain
22	chr9:8449800-8460000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:8449800-8460600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:8450200-8457600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:8450400-8456200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:8450400-8457800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:8451400-8456200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:8451400-8457600	Weak transcription	Brain Substantia Nigra	brain
29	chr9:8451400-8460000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:8451400-8492000	Weak transcription	Psoas Muscle	Psoas
31	chr9:8451600-8453400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:8451800-8453400	Weak transcription	Fetal Lung	lung
33	chr9:8451800-8456600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:8451800-8457600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:8451800-8464800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr9:8452400-8475800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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