Variant report

Variant	rs6584004
Chromosome Location	chr10:97268858-97268859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10882606	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10882608	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10882611	0.86[JPT][hapmap]
rs11188338	0.87[ASN][1000 genomes]
rs11188346	0.86[JPT][hapmap]
rs11188349	0.86[JPT][hapmap]
rs12254959	0.80[ASN][1000 genomes]
rs12776562	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1326932	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs1326934	0.83[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1819288	0.81[ASN][1000 genomes]
rs4146489	0.83[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4146490	0.83[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4572071	0.86[JPT][hapmap];0.83[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	esv1808679	chr10:97266478-97316855	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6584004	CRTAC1	cis	cerebellum	SCAN
rs6584004	AVPI1	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97249800-97274000	Weak transcription	Spleen	Spleen
2	chr10:97256800-97273200	Weak transcription	HSMM	muscle
3	chr10:97259400-97269600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:97260000-97269000	Enhancers	Left Ventricle	heart
5	chr10:97260000-97272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:97260000-97278400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:97260800-97269400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr10:97260800-97272800	Weak transcription	Esophagus	oesophagus
9	chr10:97261800-97271200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:97262000-97271800	Weak transcription	HMEC	breast
11	chr10:97262400-97271000	Weak transcription	Lung	lung
12	chr10:97262400-97275000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr10:97262400-97278400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr10:97265200-97271000	Weak transcription	Right Ventricle	heart
15	chr10:97265200-97272000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:97265400-97270800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:97266400-97271000	Weak transcription	Brain Angular Gyrus	brain
18	chr10:97266400-97272200	Weak transcription	Fetal Brain Male	brain
19	chr10:97266400-97272800	Weak transcription	Fetal Brain Female	brain
20	chr10:97266400-97273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr10:97267200-97271000	Weak transcription	Gastric	stomach
22	chr10:97267600-97275000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr10:97267800-97269000	Enhancers	Small Intestine	intestine
24	chr10:97267800-97269400	Enhancers	Fetal Intestine Large	intestine
25	chr10:97267800-97269400	Enhancers	Fetal Intestine Small	intestine
26	chr10:97268000-97269000	Enhancers	Ovary	ovary
27	chr10:97268000-97269000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr10:97268000-97269000	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr10:97268000-97269000	Enhancers	HSMMtube	muscle
30	chr10:97268000-97269200	Enhancers	Brain Anterior Caudate	brain
31	chr10:97268000-97269200	Enhancers	Stomach Mucosa	stomach
32	chr10:97268000-97269400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:97268000-97269600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr10:97268200-97269000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr10:97268200-97269000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr10:97268200-97269000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr10:97268200-97269000	Enhancers	Liver	Liver
38	chr10:97268200-97269000	Enhancers	Fetal Kidney	kidney
39	chr10:97268200-97269000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr10:97268200-97269200	Enhancers	Adipose Nuclei	Adipose
41	chr10:97268200-97269400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr10:97268200-97269400	Enhancers	Duodenum Mucosa	Duodenum
43	chr10:97268200-97269600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr10:97268200-97269600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr10:97268200-97269600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr10:97268200-97269600	Enhancers	Fetal Lung	lung
47	chr10:97268200-97269600	Enhancers	Fetal Stomach	stomach
48	chr10:97268200-97269600	Enhancers	HepG2	liver
49	chr10:97268200-97269800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr10:97268200-97270000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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