Variant report

Variant	rs1029499
Chromosome Location	chr11:17867235-17867236
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	chr11:17867031..17869895-chr11:17870240..17872137,3	MCF-7	breast:
2	chr11:17865463..17868129-chr11:17879075..17880713,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1015545	0.81[JPT][hapmap]
rs1029498	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10832863	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16934735	1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2023902	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]
rs2237931	0.81[JPT][hapmap]
rs2237932	0.81[JPT][hapmap]
rs2237933	0.81[JPT][hapmap]
rs2237934	0.81[JPT][hapmap]
rs2237939	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237941	0.81[JPT][hapmap]
rs2283247	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4402275	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59379521	0.88[ASN][1000 genomes]
rs61882413	0.89[ASN][1000 genomes]
rs61882417	0.91[ASN][1000 genomes]
rs68077051	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7110032	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7110047	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7131344	0.86[ASN][1000 genomes]
rs7484179	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][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	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	nsv1043973	chr11:17781560-17869896	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	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
4	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
rs1029499	MRGPRX1	cis	parietal	SCAN
rs1029499	USH1C	cis	cerebellum	SCAN
rs1029499	SAA3P	cis	cerebellum	SCAN
rs1029499	SAA1	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17806800-17867400	Weak transcription	Primary B cells from cord blood	blood
2	chr11:17833800-17867400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:17835000-17869400	Weak transcription	Fetal Intestine Small	intestine
4	chr11:17835200-17884200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:17838400-17971600	Weak transcription	Gastric	stomach
6	chr11:17851600-17890800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:17852200-17867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:17852200-17875800	Weak transcription	Esophagus	oesophagus
9	chr11:17853000-17870800	Weak transcription	Spleen	Spleen
10	chr11:17853800-17882400	Weak transcription	Pancreas	Pancrea
11	chr11:17854400-17867400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:17858800-17893200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr11:17860000-17873600	Weak transcription	Right Ventricle	heart
14	chr11:17861400-17867400	Weak transcription	Left Ventricle	heart
15	chr11:17862000-17867400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:17862200-17867400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:17862200-17868200	Weak transcription	Brain Angular Gyrus	brain
18	chr11:17862200-17868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:17862200-17889000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:17862200-17895400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr11:17862400-17867400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:17862400-17867600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:17862400-17867800	Weak transcription	Thymus	Thymus
24	chr11:17863200-17868000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:17863400-17867800	Weak transcription	Fetal Muscle Leg	muscle
26	chr11:17863800-17867400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:17863800-17886200	Weak transcription	Fetal Intestine Large	intestine
28	chr11:17863800-17939200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:17864200-17868200	Weak transcription	Fetal Thymus	thymus
30	chr11:17864400-17894600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:17864400-17944800	Weak transcription	Ovary	ovary
32	chr11:17864800-17899400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:17865000-17884400	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:17865400-17871800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr11:17865600-17867600	Weak transcription	Lung	lung
36	chr11:17866000-17868000	Strong transcription	HepG2	liver
37	chr11:17866000-17894600	Weak transcription	Adipose Nuclei	Adipose
38	chr11:17866200-17877400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:17866200-17894600	Weak transcription	Liver	Liver
40	chr11:17866400-17868600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:17866400-17869000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:17866400-17869000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:17866600-17868000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:17866600-17868000	Enhancers	Hela-S3	cervix
45	chr11:17866600-17868000	Enhancers	HSMM	muscle
46	chr11:17866600-17868200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:17866600-17868400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr11:17866600-17868600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr11:17866600-17868600	Enhancers	HMEC	breast
50	chr11:17866600-17868800	Enhancers	NHLF	lung

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