Variant report

Variant	rs4850925
Chromosome Location	chr2:100910578-100910579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100907987..100912107-chr2:100920120..100922978,3	MCF-7	breast:
2	chr2:100900693..100917248-chr2:100932005..100942326,51	MCF-7	breast:
3	chr2:100907126..100910810-chr2:100936315..100940527,7	K562	blood:
4	chr2:100899535..100901575-chr2:100909309..100912532,4	K562	blood:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10174820	0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10176062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10176143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10195018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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]
rs10201565	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10201669	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123822	0.82[ASN][1000 genomes]
rs11890655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615454	0.85[JPT][hapmap]
rs13391517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13400045	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13409545	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023901	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748928	0.83[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851279	0.82[JPT][hapmap]
rs55759234	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542922	0.82[JPT][hapmap]
rs6542925	0.83[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7556910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764828	0.83[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4850925	IL18R1	cis	cerebellum	SCAN
rs4850925	C2orf55	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100898400-100915600	Weak transcription	Right Atrium	heart
2	chr2:100898800-100915000	Weak transcription	Adipose Nuclei	Adipose
3	chr2:100900200-100919000	Strong transcription	Fetal Brain Female	brain
4	chr2:100900800-100926600	Weak transcription	Right Ventricle	heart
5	chr2:100901000-100937000	Weak transcription	Fetal Brain Male	brain
6	chr2:100903200-100918000	Weak transcription	Liver	Liver
7	chr2:100903400-100930800	Weak transcription	Brain Substantia Nigra	brain
8	chr2:100903600-100914400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:100903600-100926200	Weak transcription	Fetal Kidney	kidney
10	chr2:100906600-100911400	Strong transcription	Brain Germinal Matrix	brain
11	chr2:100906800-100910600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:100906800-100910600	Enhancers	Placenta	Placenta
13	chr2:100907000-100912000	Weak transcription	Aorta	Aorta
14	chr2:100908000-100919400	Weak transcription	Spleen	Spleen
15	chr2:100908200-100917800	Weak transcription	Lung	lung
16	chr2:100908400-100914400	Weak transcription	Esophagus	oesophagus
17	chr2:100908400-100917600	Weak transcription	Fetal Stomach	stomach
18	chr2:100908600-100915800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr2:100908800-100910800	Genic enhancers	K562	blood
20	chr2:100908800-100912200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:100908800-100926600	Weak transcription	Gastric	stomach
22	chr2:100909000-100910800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:100909000-100911000	Enhancers	Hela-S3	cervix
24	chr2:100909000-100913600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:100909000-100915000	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:100909000-100920600	Weak transcription	Fetal Intestine Small	intestine
27	chr2:100909200-100913600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:100909200-100914000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:100909400-100910800	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr2:100909400-100911000	Strong transcription	Brain Hippocampus Middle	brain
31	chr2:100909400-100911200	Strong transcription	Brain Anterior Caudate	brain
32	chr2:100909600-100911000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:100909800-100911000	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:100909800-100911200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:100909800-100914200	Strong transcription	Pancreas	Pancrea
36	chr2:100910000-100911200	Strong transcription	Brain Angular Gyrus	brain
37	chr2:100910000-100911200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:100910000-100911200	Strong transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:100910000-100913000	Strong transcription	Brain Cingulate Gyrus	brain
40	chr2:100910200-100911000	Strong transcription	Ovary	ovary
41	chr2:100910200-100920000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:100910200-100920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:100910400-100910800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:100910400-100910800	Strong transcription	Left Ventricle	heart
45	chr2:100910400-100910800	Genic enhancers	A549	lung
46	chr2:100910400-100911200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:100910400-100918200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:100910400-100925800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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