Variant report

Variant	rs7912249
Chromosome Location	chr10:97272774-97272775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97255064..97257617-chr10:97271622..97273423,2	K562	blood:
2	chr10:97272650..97274953-chr10:97291349..97294026,2	K562	blood:
3	chr10:97271514..97273430-chr10:97278974..97280871,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10736089	1.00[ASW][hapmap];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];0.96[MKK][hapmap];1.00[TSI][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]
rs10786216	1.00[ASN][1000 genomes]
rs1326931	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1326933	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1326935	1.00[CHD][hapmap];0.96[GIH][hapmap]
rs1326937	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1326938	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1326939	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]
rs1359723	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1359724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409708	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1409715	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1536441	1.00[JPT][hapmap]
rs1536447	1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[ASN][1000 genomes]
rs1571132	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1609588	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1819287	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3927490	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4244315	0.83[GIH][hapmap]
rs4457684	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4466758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498913	1.00[ASW][hapmap];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];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4592368	1.00[ASW][hapmap];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];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4617517	0.93[ASN][1000 genomes]
rs4638246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4918945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4918946	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6584005	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][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]
rs6584008	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7081926	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7904778	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910345	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915173	0.93[ASN][1000 genomes]
rs7921696	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs943339	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs943340	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs943348	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7912249	CRTAC1	cis	cerebellum	SCAN
rs7912249	IDE	cis	cerebellum	SCAN
rs7912249	KIF11	cis	parietal	SCAN

Chromatin state (count:73 , 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	chr10:97260000-97272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:97260000-97278400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:97260800-97272800	Weak transcription	Esophagus	oesophagus
6	chr10:97262400-97275000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:97262400-97278400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr10:97266400-97272800	Weak transcription	Fetal Brain Female	brain
9	chr10:97266400-97273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:97267600-97275000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr10:97268800-97272800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr10:97268800-97273000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:97269000-97272800	Weak transcription	Small Intestine	intestine
14	chr10:97269000-97273000	Weak transcription	Ovary	ovary
15	chr10:97269000-97273000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:97269000-97277200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:97269000-97282600	Weak transcription	Fetal Kidney	kidney
18	chr10:97269200-97272800	Weak transcription	HUVEC	blood vessel
19	chr10:97269200-97273800	Weak transcription	Adipose Nuclei	Adipose
20	chr10:97269200-97277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr10:97269400-97272800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr10:97269400-97273000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:97269400-97273000	Weak transcription	Fetal Intestine Large	intestine
24	chr10:97269400-97273200	Weak transcription	NH-A	brain
25	chr10:97269400-97277200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr10:97269600-97273400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:97269600-97277200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr10:97270200-97274600	Enhancers	HepG2	liver
29	chr10:97270600-97272800	Enhancers	Brain Anterior Caudate	brain
30	chr10:97270600-97273800	Enhancers	Aorta	Aorta
31	chr10:97270600-97278200	Enhancers	Rectal Smooth Muscle	rectum
32	chr10:97270600-97278600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr10:97270600-97279200	Enhancers	Left Ventricle	heart
34	chr10:97270600-97279200	Enhancers	Right Atrium	heart
35	chr10:97270600-97279200	Enhancers	Stomach Mucosa	stomach
36	chr10:97270600-97283400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr10:97270800-97275000	Enhancers	Brain Cingulate Gyrus	brain
38	chr10:97270800-97275000	Enhancers	Brain Hippocampus Middle	brain
39	chr10:97270800-97275600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr10:97270800-97275800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr10:97271000-97273600	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr10:97271000-97273800	Enhancers	Pancreas	Pancrea
43	chr10:97271000-97274200	Enhancers	Lung	lung
44	chr10:97271000-97274600	Enhancers	Brain Substantia Nigra	brain
45	chr10:97271000-97275200	Enhancers	Brain Angular Gyrus	brain
46	chr10:97271000-97281200	Enhancers	Right Ventricle	heart
47	chr10:97271400-97275000	Enhancers	Liver	Liver
48	chr10:97271400-97275800	Weak transcription	Gastric	stomach
49	chr10:97271400-97279800	Enhancers	Fetal Muscle Leg	muscle
50	chr10:97271400-97279800	Enhancers	Skeletal Muscle Male	skeletal muscle

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