Variant report

Variant	rs2662260
Chromosome Location	chr5:98122187-98122188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98113211..98117452-chr5:98120749..98124460,5	MCF-7	breast:
2	chr5:98105419..98111417-chr5:98120321..98126739,11	MCF-7	breast:
3	chr5:98121084..98123480-chr5:98124476..98127082,2	K562	blood:
4	chr5:98107013..98112208-chr5:98121949..98125778,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246763	Chromatin interaction
ENSG00000174136	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10515283	1.00[ASN][1000 genomes]
rs1828168	1.00[ASN][1000 genomes]
rs2545677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545680	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545688	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545727	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545728	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545729	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2617508	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617512	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2617515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662255	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2662256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662259	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2662261	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2859485	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773677	1.00[ASN][1000 genomes]
rs72773692	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773694	0.89[AMR][1000 genomes];0.93[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2662260	PDGFD	trans	lymphoblastoid	seeQTL
rs2662260	RGMB	cis	normal skin	skin_eQTL
rs2662260	RGMB	cis	lesional skin	skin_eQTL
rs2662260	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2662260	RGMB	cis	uninvolved skin	skin_eQTL
rs2662260	SLCO4C1	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98110200-98125200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
2	chr5:98110800-98123200	Weak transcription	Aorta	Aorta
3	chr5:98111000-98128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
6	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:98112400-98122400	Weak transcription	Fetal Heart	heart
8	chr5:98114800-98131400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:98115000-98122200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:98115000-98125400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:98115600-98123200	Weak transcription	Primary T cells from cord blood	blood
12	chr5:98115800-98123200	Weak transcription	Right Atrium	heart
13	chr5:98115800-98123800	Genic enhancers	NHEK	skin
14	chr5:98116600-98125200	Genic enhancers	Osteobl	bone
15	chr5:98116800-98123200	Weak transcription	HepG2	liver
16	chr5:98116800-98127600	Weak transcription	Hela-S3	cervix
17	chr5:98117000-98128600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:98117600-98132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:98117800-98125000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:98117800-98125200	Genic enhancers	Fetal Muscle Leg	muscle
21	chr5:98117800-98125600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:98117800-98128000	Genic enhancers	HSMM	muscle
23	chr5:98118200-98122400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr5:98118200-98123800	Enhancers	Brain Substantia Nigra	brain
25	chr5:98118400-98123400	Enhancers	Brain Hippocampus Middle	brain
26	chr5:98118400-98131800	Weak transcription	A549	lung
27	chr5:98118600-98122600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr5:98118600-98123400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
29	chr5:98118600-98124400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr5:98118800-98122200	Enhancers	Brain Cingulate Gyrus	brain
31	chr5:98118800-98122800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:98118800-98123400	Enhancers	Brain Angular Gyrus	brain
33	chr5:98118800-98123600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:98119000-98126000	Enhancers	Colon Smooth Muscle	Colon
35	chr5:98119200-98122200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr5:98119200-98122400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:98119200-98123000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:98119200-98128800	Weak transcription	Spleen	Spleen
39	chr5:98119200-98129000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:98119800-98122400	Enhancers	Fetal Brain Female	brain
41	chr5:98119800-98122800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
42	chr5:98119800-98122800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:98119800-98123800	Enhancers	Colonic Mucosa	Colon
44	chr5:98120000-98122400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr5:98120000-98122600	Weak transcription	Esophagus	oesophagus
46	chr5:98120000-98122600	Enhancers	Fetal Stomach	stomach
47	chr5:98120000-98123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:98120000-98124600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr5:98120000-98125000	Enhancers	Small Intestine	intestine
50	chr5:98120200-98122200	Enhancers	Skeletal Muscle Male	skeletal muscle

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