Variant report

Variant	rs2490438
Chromosome Location	chr1:161936788-161936789
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	chr1:161930299..161933579-chr1:161936760..161939444,3	K562	blood:
2	chr1:161934463..161936874-chr1:161938543..161943088,4	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11579627	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2490433	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2490436	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2490437	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2490439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490441	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2499844	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2499851	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2499853	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3002626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1007108	chr1:161925814-162002917	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2490438	KIRREL	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161897800-161940000	Weak transcription	Brain Germinal Matrix	brain
2	chr1:161902800-161943400	Weak transcription	Esophagus	oesophagus
3	chr1:161904800-161956600	Weak transcription	Fetal Brain Male	brain
4	chr1:161911000-161937200	Weak transcription	Gastric	stomach
5	chr1:161911600-161939400	Weak transcription	HepG2	liver
6	chr1:161912600-161941600	Weak transcription	Fetal Kidney	kidney
7	chr1:161925000-161937600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:161926200-161939400	Weak transcription	Fetal Heart	heart
9	chr1:161926200-161942200	Weak transcription	Right Ventricle	heart
10	chr1:161927000-161944000	Weak transcription	Colonic Mucosa	Colon
11	chr1:161927800-161937600	Strong transcription	Primary B cells from cord blood	blood
12	chr1:161928200-161938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:161928200-161938800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:161928400-161941800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:161928600-161939000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:161929000-161943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:161929200-161944000	Weak transcription	Ovary	ovary
18	chr1:161931000-161938400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:161931000-161939600	Weak transcription	Fetal Brain Female	brain
20	chr1:161931000-161943200	Weak transcription	Placenta	Placenta
21	chr1:161931200-161937000	Weak transcription	Lung	lung
22	chr1:161931200-161940400	Weak transcription	Fetal Thymus	thymus
23	chr1:161931200-161940600	Weak transcription	Fetal Intestine Large	intestine
24	chr1:161931200-161942400	Weak transcription	Spleen	Spleen
25	chr1:161931200-161943400	Weak transcription	Psoas Muscle	Psoas
26	chr1:161931400-161943400	Weak transcription	K562	blood
27	chr1:161931800-161942800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:161932000-161936800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:161932200-161939400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:161932400-161937000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:161932400-161939200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:161932400-161939400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:161932400-161942200	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:161932400-161955400	Weak transcription	Brain Substantia Nigra	brain
35	chr1:161932600-161938000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:161932600-161938200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:161932600-161939200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:161932600-161940200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:161932600-161940400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:161932600-161940400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:161932600-161940400	Weak transcription	Brain Anterior Caudate	brain
42	chr1:161932600-161943200	Weak transcription	Adipose Nuclei	Adipose
43	chr1:161932600-161943200	Weak transcription	Right Atrium	heart
44	chr1:161932600-161943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:161932800-161938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:161932800-161940200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:161932800-161943200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:161932800-161944000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:161933000-161938000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:161933000-161938600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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