Variant report

Variant	rs4592368
Chromosome Location	chr10:97277876-97277877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97277519..97280426-chr10:97289369..97291949,2	K562	blood:

Extended variants
information (count: 43 )
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];1.00[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]
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];0.99[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409708	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[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];1.00[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];0.99[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];1.00[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]
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];1.00[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];0.96[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];1.00[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]
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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910345	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7912249	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]
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];1.00[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:2 , 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
2	esv3328695	chr10:97277817-97278168	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4592368	CRTAC1	cis	cerebellum	SCAN
rs4592368	IDE	cis	cerebellum	SCAN
rs4592368	KIF11	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97260000-97278400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:97262400-97278400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:97269000-97282600	Weak transcription	Fetal Kidney	kidney
4	chr10:97270600-97278200	Enhancers	Rectal Smooth Muscle	rectum
5	chr10:97270600-97278600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr10:97270600-97279200	Enhancers	Left Ventricle	heart
7	chr10:97270600-97279200	Enhancers	Right Atrium	heart
8	chr10:97270600-97279200	Enhancers	Stomach Mucosa	stomach
9	chr10:97270600-97283400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr10:97271000-97281200	Enhancers	Right Ventricle	heart
11	chr10:97271400-97279800	Enhancers	Fetal Muscle Leg	muscle
12	chr10:97271400-97279800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr10:97271600-97279800	Enhancers	Fetal Heart	heart
14	chr10:97271600-97284600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr10:97272800-97278600	Enhancers	HUVEC	blood vessel
16	chr10:97273400-97279800	Enhancers	Colon Smooth Muscle	Colon
17	chr10:97273600-97284000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr10:97274200-97278600	Weak transcription	Fetal Lung	lung
19	chr10:97274200-97279200	Enhancers	Pancreas	Pancrea
20	chr10:97274400-97280400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr10:97275200-97279800	Enhancers	Brain Anterior Caudate	brain
22	chr10:97275600-97279400	Enhancers	Aorta	Aorta
23	chr10:97275800-97278600	Weak transcription	Spleen	Spleen
24	chr10:97275800-97279800	Enhancers	HepG2	liver
25	chr10:97276000-97278200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr10:97276200-97278000	Enhancers	Brain Substantia Nigra	brain
27	chr10:97276200-97279400	Enhancers	K562	blood
28	chr10:97276400-97279200	Enhancers	HSMMtube	muscle
29	chr10:97276400-97279600	Enhancers	Liver	Liver
30	chr10:97276600-97278000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr10:97276600-97279200	Enhancers	Gastric	stomach
32	chr10:97276600-97279600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr10:97276600-97279800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:97276600-97283400	Enhancers	Fetal Brain Male	brain
35	chr10:97276800-97278800	Enhancers	Fetal Intestine Small	intestine
36	chr10:97276800-97280000	Enhancers	Fetal Stomach	stomach
37	chr10:97277000-97278000	Enhancers	Esophagus	oesophagus
38	chr10:97277000-97278800	Enhancers	Brain Hippocampus Middle	brain
39	chr10:97277000-97279000	Enhancers	Psoas Muscle	Psoas
40	chr10:97277000-97279000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr10:97277000-97279200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr10:97277000-97279200	Enhancers	Brain Germinal Matrix	brain
43	chr10:97277000-97279200	Enhancers	Fetal Intestine Large	intestine
44	chr10:97277000-97284200	Enhancers	Fetal Brain Female	brain
45	chr10:97277200-97278000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr10:97277200-97278000	Enhancers	Ovary	ovary
47	chr10:97277200-97278400	Enhancers	NH-A	brain
48	chr10:97277200-97278800	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr10:97277200-97279000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr10:97277200-97279200	Enhancers	Brain Inferior Temporal Lobe	brain

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