Variant report

Variant	rs2023902
Chromosome Location	chr11:17874226-17874227
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17804443..17806483-chr11:17873609..17875464,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1029498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1029499	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10832863	0.93[CEU][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16934735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237939	0.86[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2283247	1.00[CEU][hapmap];0.87[YRI][hapmap];0.99[EUR][1000 genomes]
rs4402275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59143224	0.92[ASN][1000 genomes]
rs61882415	0.92[ASN][1000 genomes]
rs61882416	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs67445779	1.00[ASN][1000 genomes]
rs68077051	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110032	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7110047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72873810	0.97[ASN][1000 genomes]
rs7484179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832078	chr11:17780503-17953521	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2023902	MRGPRX1	cis	parietal	SCAN
rs2023902	SAA3P	cis	cerebellum	SCAN
rs2023902	SAA1	cis	parietal	SCAN
rs2023902	USH1C	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17835200-17884200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:17838400-17971600	Weak transcription	Gastric	stomach
3	chr11:17851600-17890800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr11:17852200-17875800	Weak transcription	Esophagus	oesophagus
5	chr11:17853800-17882400	Weak transcription	Pancreas	Pancrea
6	chr11:17858800-17893200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:17862200-17889000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:17862200-17895400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr11:17863800-17886200	Weak transcription	Fetal Intestine Large	intestine
10	chr11:17863800-17939200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:17864400-17894600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:17864400-17944800	Weak transcription	Ovary	ovary
13	chr11:17864800-17899400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:17865000-17884400	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:17866000-17894600	Weak transcription	Adipose Nuclei	Adipose
16	chr11:17866200-17877400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:17866200-17894600	Weak transcription	Liver	Liver
18	chr11:17866600-17888800	Weak transcription	Dnd41	blood
19	chr11:17866600-17895400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:17867000-17877400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:17867400-17876000	Weak transcription	GM12878-XiMat	blood
22	chr11:17867800-17890200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:17868000-17878000	Weak transcription	HepG2	liver
24	chr11:17868400-17895200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:17868600-17878400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:17868600-17882400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:17868600-17894800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:17868600-17914000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:17868800-17882400	Weak transcription	Aorta	Aorta
30	chr11:17868800-17887600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:17868800-17894600	Weak transcription	Brain Anterior Caudate	brain
32	chr11:17868800-17894800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:17868800-17895200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:17869000-17878000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:17869000-17895400	Weak transcription	Lung	lung
36	chr11:17869000-17909600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr11:17869000-17916400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:17869200-17877600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr11:17869400-17887600	Weak transcription	Fetal Thymus	thymus
40	chr11:17870600-17874800	Weak transcription	Thymus	Thymus
41	chr11:17870600-17881400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr11:17871000-17879000	Weak transcription	K562	blood
43	chr11:17871200-17876200	Strong transcription	Primary T cells from cord blood	blood
44	chr11:17871600-17875000	Strong transcription	Primary B cells from cord blood	blood
45	chr11:17871600-17877600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:17872400-17877400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:17872600-17875200	Enhancers	Psoas Muscle	Psoas
48	chr11:17872600-17877600	Weak transcription	Brain Germinal Matrix	brain
49	chr11:17872600-17926600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:17872800-17875200	Enhancers	Skeletal Muscle Female	skeletal muscle

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