Variant report

Variant	rs2662258
Chromosome Location	chr5:98125530-98125531
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98121084..98123480-chr5:98124476..98127082,2	K562	blood:
2	chr5:98124225..98126572-chr5:98127471..98130049,2	K562	blood:
3	chr5:98124398..98126468-chr5:98128299..98131960,3	MCF-7	breast:
4	chr5:98123018..98126275-chr5:98130087..98132367,4	MCF-7	breast:
5	chr5:98105419..98111417-chr5:98120321..98126739,11	MCF-7	breast:
6	chr5:98107013..98112208-chr5:98121949..98125778,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174136	Chromatin interaction
ENSG00000246763	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1002859	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs13541	0.90[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs1508793	0.86[CHD][hapmap]
rs161937	0.87[ASW][hapmap]
rs1828169	0.89[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs1911904	0.81[CHD][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs1979980	0.86[CHD][hapmap]
rs2250807	0.85[CHB][hapmap]
rs2545676	0.96[CEU][hapmap];0.90[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331550	0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs331551	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331552	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs692759	0.87[ASW][hapmap]
rs970079	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2662258	RHOBTB3	cis	cerebellum	SCAN
rs2662258	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2662258	RGMB	cis	uninvolved skin	skin_eQTL
rs2662258	RGMB	cis	normal skin	skin_eQTL
rs2662258	RGMB	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98111000-98128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
4	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:98114800-98131400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:98116800-98127600	Weak transcription	Hela-S3	cervix
7	chr5:98117000-98128600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:98117600-98132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:98117800-98125600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:98117800-98128000	Genic enhancers	HSMM	muscle
11	chr5:98118400-98131800	Weak transcription	A549	lung
12	chr5:98119000-98126000	Enhancers	Colon Smooth Muscle	Colon
13	chr5:98119200-98128800	Weak transcription	Spleen	Spleen
14	chr5:98119200-98129000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:98120200-98126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:98120800-98127200	Enhancers	Duodenum Mucosa	Duodenum
17	chr5:98121000-98127200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:98121200-98128800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:98121600-98128800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:98121800-98128600	Genic enhancers	Muscle Satellite Cultured Cells	--
21	chr5:98122000-98129000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:98122200-98132000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:98122400-98127200	Strong transcription	NH-A	brain
24	chr5:98122400-98128800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:98122600-98127400	Weak transcription	Adipose Nuclei	Adipose
26	chr5:98122600-98128800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr5:98122800-98128000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:98123000-98132400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:98123200-98128800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:98123200-98129000	Weak transcription	GM12878-XiMat	blood
31	chr5:98123400-98126000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:98123400-98126400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:98123400-98126800	Weak transcription	Brain Angular Gyrus	brain
34	chr5:98123400-98128800	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:98123400-98129000	Weak transcription	Right Ventricle	heart
36	chr5:98123600-98126600	Weak transcription	Fetal Kidney	kidney
37	chr5:98123600-98128600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:98123600-98128800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:98123600-98128800	Weak transcription	Brain Germinal Matrix	brain
40	chr5:98123600-98128800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:98123600-98128800	Weak transcription	Fetal Brain Female	brain
42	chr5:98123800-98126800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr5:98123800-98126800	Weak transcription	Fetal Stomach	stomach
44	chr5:98123800-98127000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:98123800-98127800	Weak transcription	NHEK	skin
46	chr5:98123800-98128000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr5:98123800-98128600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:98123800-98128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:98123800-98128800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:98123800-98128800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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