Variant report

Variant	rs10084416
Chromosome Location	chr2:205318602-205318603
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:205317459..205320428-chr2:205333008..205336253,3	K562	blood:
2	chr2:205314792..205317401-chr2:205318306..205319999,2	K562	blood:
3	chr2:205317294..205319471-chr2:205340816..205343787,2	K562	blood:
4	chr2:205317299..205320276-chr2:205333008..205336367,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10490267	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10932063	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1156249	1.00[ASN][1000 genomes]
rs11690070	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12472876	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12616166	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12990859	0.81[ASN][1000 genomes]
rs13010221	0.90[ASN][1000 genomes]
rs13024043	0.93[ASN][1000 genomes]
rs1374708	0.98[ASN][1000 genomes]
rs1374709	0.87[ASN][1000 genomes]
rs1447488	0.96[ASN][1000 genomes]
rs1447490	0.93[ASN][1000 genomes]
rs1447493	0.93[ASN][1000 genomes]
rs1447495	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1550909	1.00[JPT][hapmap]
rs17637637	0.93[ASN][1000 genomes]
rs34157021	0.87[ASN][1000 genomes]
rs34368384	0.92[ASN][1000 genomes]
rs35071164	0.83[ASN][1000 genomes]
rs35207649	0.81[ASN][1000 genomes]
rs4675457	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71427747	0.92[ASN][1000 genomes]
rs7602656	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs921163	1.00[JPT][hapmap]
rs959032	0.93[ASN][1000 genomes]
rs959033	0.93[ASN][1000 genomes]
rs9679305	0.81[AFR][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	nsv964353	chr2:205303005-205473935	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv34706	chr2:205309211-205348724	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10084416	ICA1L	cis	cerebellum	SCAN
rs10084416	CFLAR	cis	cerebellum	SCAN
rs10084416	ICOS	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:205314000-205320000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr2:205314600-205319800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:205315600-205318800	Weak transcription	Brain Anterior Caudate	brain
4	chr2:205316600-205320200	Enhancers	Fetal Brain Male	brain
5	chr2:205316600-205320400	Enhancers	Fetal Intestine Small	intestine
6	chr2:205316800-205319000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:205316800-205319200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:205316800-205319600	Enhancers	Fetal Kidney	kidney
9	chr2:205316800-205320200	Enhancers	Fetal Muscle Leg	muscle
10	chr2:205317200-205319200	Enhancers	NHLF	lung
11	chr2:205317200-205319400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:205317200-205319800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:205317200-205320000	Enhancers	Fetal Brain Female	brain
14	chr2:205317200-205320000	Enhancers	K562	blood
15	chr2:205317400-205320200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:205317600-205319200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:205317800-205319000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:205317800-205319200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:205317800-205319200	Enhancers	HUVEC	blood vessel
20	chr2:205317800-205319200	Enhancers	NH-A	brain
21	chr2:205317800-205319200	Enhancers	NHDF-Ad	bronchial
22	chr2:205317800-205319400	Enhancers	A549	lung
23	chr2:205318000-205318800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:205318200-205319000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:205318200-205319200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:205318200-205319200	Enhancers	Left Ventricle	heart
27	chr2:205318200-205319400	Enhancers	Brain Germinal Matrix	brain
28	chr2:205318200-205319600	Enhancers	Fetal Heart	heart
29	chr2:205318200-205319800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:205318200-205320000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:205318200-205320000	Enhancers	Fetal Intestine Large	intestine
32	chr2:205318200-205320000	Enhancers	Fetal Stomach	stomach
33	chr2:205318400-205318800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr2:205318400-205318800	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr2:205318400-205318800	Enhancers	Right Atrium	heart
36	chr2:205318400-205319000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:205318400-205319000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:205318400-205319000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:205318400-205319000	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr2:205318400-205319000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr2:205318400-205319000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:205318400-205319000	Enhancers	Osteobl	bone
43	chr2:205318400-205319200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:205318400-205319200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:205318400-205319200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:205318400-205319200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr2:205318400-205319200	Flanking Active TSS	Fetal Lung	lung
48	chr2:205318400-205319200	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr2:205318400-205319400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:205318400-205319600	Enhancers	Brain Substantia Nigra	brain

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