Variant report

Variant	rs2545680
Chromosome Location	chr5:98131883-98131884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98122831..98123704-chr5:98131769..98132290,2	MCF-7	breast:
2	chr5:98129808..98132282-chr5:98134081..98135788,2	K562	blood:
3	chr5:98123018..98126275-chr5:98130087..98132367,4	MCF-7	breast:
4	chr5:98131550..98132070-chr6:141289515..141290035,2	MCF-7	breast:
5	chr5:98105450..98112138-chr5:98128603..98138411,14	MCF-7	breast:
6	chr5:98124398..98126468-chr5:98128299..98131960,3	MCF-7	breast:
7	chr5:98126420..98128371-chr5:98130230..98131989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174136	Chromatin interaction
ENSG00000246763	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10515283	1.00[ASN][1000 genomes]
rs150935	1.00[YRI][hapmap]
rs161729	1.00[YRI][hapmap]
rs161732	0.82[YRI][hapmap]
rs161736	1.00[YRI][hapmap]
rs161739	1.00[YRI][hapmap]
rs161746	1.00[YRI][hapmap]
rs161750	1.00[YRI][hapmap]
rs161940	1.00[YRI][hapmap]
rs161957	1.00[YRI][hapmap]
rs1828168	1.00[ASN][1000 genomes]
rs2545677	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]
rs2545688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545729	0.91[EUR][1000 genomes]
rs2545735	1.00[YRI][hapmap]
rs2578576	1.00[YRI][hapmap]
rs2578577	1.00[YRI][hapmap]
rs2617508	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617512	0.90[EUR][1000 genomes]
rs2617515	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662255	0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs2662256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2662259	0.91[EUR][1000 genomes]
rs2662260	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]
rs2662261	0.91[EUR][1000 genomes]
rs2859485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325195	1.00[YRI][hapmap]
rs325199	1.00[YRI][hapmap]
rs325203	1.00[YRI][hapmap]
rs325204	1.00[YRI][hapmap]
rs325208	1.00[YRI][hapmap]
rs325209	0.82[YRI][hapmap]
rs326481	0.82[YRI][hapmap]
rs326482	0.82[YRI][hapmap]
rs331542	1.00[YRI][hapmap]
rs34498	0.82[YRI][hapmap]
rs72773677	1.00[ASN][1000 genomes]
rs72773692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs2545680	RGMB	cis	lesional skin	skin_eQTL
rs2545680	SLCO4C1	cis	cerebellum	SCAN
rs2545680	RGMB	cis	uninvolved skin	skin_eQTL
rs2545680	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2545680	RGMB	cis	normal skin	skin_eQTL
rs2545680	SLCO4C1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:98117600-98132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:98122200-98132000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:98123000-98132400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:98123800-98132000	Weak transcription	Primary T cells from cord blood	blood
6	chr5:98123800-98136800	Weak transcription	Fetal Brain Male	brain
7	chr5:98123800-98140600	Weak transcription	Brain Substantia Nigra	brain
8	chr5:98124000-98132000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:98124000-98132000	Weak transcription	Fetal Lung	lung
10	chr5:98125200-98132000	Genic enhancers	NHDF-Ad	bronchial
11	chr5:98125600-98132000	Weak transcription	Stomach Mucosa	stomach
12	chr5:98129200-98132200	Weak transcription	Hela-S3	cervix
13	chr5:98129400-98132000	Weak transcription	Spleen	Spleen
14	chr5:98129400-98132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:98129400-98132200	Weak transcription	HMEC	breast
16	chr5:98129400-98132600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:98129400-98132800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:98129400-98132800	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:98129400-98141200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:98129600-98136000	Weak transcription	Esophagus	oesophagus
21	chr5:98130000-98132000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:98130000-98132200	Weak transcription	Ovary	ovary
23	chr5:98130000-98132200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr5:98130000-98132400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:98130000-98136600	Weak transcription	Aorta	Aorta
26	chr5:98130000-98137600	Weak transcription	Adipose Nuclei	Adipose
27	chr5:98130200-98132000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:98130200-98132800	Weak transcription	Brain Germinal Matrix	brain
29	chr5:98130200-98136200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:98130200-98139200	Weak transcription	GM12878-XiMat	blood
31	chr5:98130400-98132200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:98130400-98132600	Genic enhancers	Fetal Muscle Leg	muscle
33	chr5:98130600-98132000	Enhancers	Psoas Muscle	Psoas
34	chr5:98130600-98136600	Weak transcription	Fetal Intestine Large	intestine
35	chr5:98130600-98140200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:98130800-98132600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:98130800-98132600	Enhancers	NHLF	lung
38	chr5:98130800-98136400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:98130800-98138800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:98130800-98138800	Weak transcription	Fetal Stomach	stomach
41	chr5:98130800-98140200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:98131000-98132200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr5:98131000-98132600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:98131000-98132800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr5:98131000-98133000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:98131200-98132200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:98131200-98132200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:98131200-98132200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr5:98131200-98132400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr5:98131200-98132600	Enhancers	Stomach Smooth Muscle	stomach

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