Variant report

Variant	rs4146490
Chromosome Location	chr10:97290539-97290540
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97277519..97280426-chr10:97289369..97291949,2	K562	blood:
2	chr10:97289605..97292487-chr10:97295547..97298455,3	K562	blood:
3	chr10:97288240..97291346-chr10:97319603..97322550,3	K562	blood:
4	chr10:97285880..97288158-chr10:97290360..97291993,2	K562	blood:
5	chr10:97262883..97265174-chr10:97289179..97291481,2	K562	blood:

Variant related genes	Relation type
ENSG00000095637	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10882609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882610	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs11188343	1.00[CEU][hapmap];0.87[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];0.95[ASN][1000 genomes]
rs12776800	0.82[JPT][hapmap]
rs1326934	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1952232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4146489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4146491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4917695	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6584004	0.83[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs6584007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918060	0.81[ASN][1000 genomes]
rs943338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4146490	CRTAC1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97278000-97294000	Weak transcription	Esophagus	oesophagus
2	chr10:97279200-97293200	Weak transcription	Fetal Lung	lung
3	chr10:97279800-97290600	Weak transcription	Fetal Muscle Leg	muscle
4	chr10:97280600-97291000	Enhancers	Colon Smooth Muscle	Colon
5	chr10:97280800-97301400	Enhancers	Fetal Heart	heart
6	chr10:97281600-97296400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:97281800-97295000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr10:97282200-97304400	Weak transcription	Brain Germinal Matrix	brain
9	chr10:97282400-97292000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr10:97282400-97292000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:97283000-97292000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:97283200-97296400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:97285200-97292400	Enhancers	Fetal Intestine Large	intestine
14	chr10:97286000-97290800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:97286200-97294800	Weak transcription	Small Intestine	intestine
16	chr10:97286200-97296000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr10:97286800-97293200	Weak transcription	Liver	Liver
18	chr10:97287800-97292800	Enhancers	Brain Cingulate Gyrus	brain
19	chr10:97288200-97291000	Enhancers	HepG2	liver
20	chr10:97288600-97291800	Weak transcription	Placenta	Placenta
21	chr10:97288800-97292400	Enhancers	Brain Anterior Caudate	brain
22	chr10:97288800-97292800	Enhancers	Right Atrium	heart
23	chr10:97288800-97293600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr10:97288800-97294400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:97289000-97291200	Enhancers	Fetal Brain Female	brain
26	chr10:97289000-97291400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:97289000-97291400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr10:97289000-97292400	Enhancers	Fetal Stomach	stomach
29	chr10:97289000-97294800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr10:97289000-97295000	Enhancers	Right Ventricle	heart
31	chr10:97289200-97290800	Enhancers	K562	blood
32	chr10:97289200-97291000	Enhancers	Brain Angular Gyrus	brain
33	chr10:97289200-97291600	Enhancers	Primary hematopoietic stem cells	blood
34	chr10:97289200-97292200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr10:97289200-97292400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr10:97289200-97292600	Enhancers	Lung	lung
37	chr10:97289200-97299200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr10:97289200-97309000	Enhancers	Left Ventricle	heart
39	chr10:97289400-97291000	Enhancers	Psoas Muscle	Psoas
40	chr10:97289400-97291200	Enhancers	Pancreas	Pancrea
41	chr10:97289400-97291800	Weak transcription	HUVEC	blood vessel
42	chr10:97289400-97292200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr10:97289400-97296200	Weak transcription	HSMMtube	muscle
44	chr10:97289400-97303800	Weak transcription	HSMM	muscle
45	chr10:97289600-97290800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr10:97289800-97291800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr10:97289800-97292600	Genic enhancers	Fetal Intestine Small	intestine
48	chr10:97289800-97293800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr10:97290000-97291600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr10:97290000-97292000	Weak transcription	Brain Inferior Temporal Lobe	brain

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