Variant report

Variant	rs13541
Chromosome Location	chr5:98131505-98131506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000246763	Chromatin interaction
ENSG00000174136	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1002859	0.81[CHD][hapmap]
rs1508793	0.81[CHD][hapmap]
rs1828169	0.83[CHD][hapmap]
rs1979980	0.81[CHD][hapmap]
rs2250807	0.83[CHB][hapmap]
rs2545676	0.84[CHB][hapmap]
rs2662258	0.90[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs331547	0.87[ASN][1000 genomes]
rs331550	0.84[CHB][hapmap]
rs331551	0.85[CHB][hapmap];0.89[CHD][hapmap]
rs970079	0.90[CHB][hapmap];0.80[JPT][hapmap];0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13541	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs13541	RGMB	cis	normal skin	skin_eQTL
rs13541	PCSK1	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
3	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:98117600-98132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:98118400-98131800	Weak transcription	A549	lung
6	chr5:98122200-98132000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:98123000-98132400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:98123800-98132000	Weak transcription	Primary T cells from cord blood	blood
9	chr5:98123800-98136800	Weak transcription	Fetal Brain Male	brain
10	chr5:98123800-98140600	Weak transcription	Brain Substantia Nigra	brain
11	chr5:98124000-98132000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr5:98124000-98132000	Weak transcription	Fetal Lung	lung
13	chr5:98125200-98132000	Genic enhancers	NHDF-Ad	bronchial
14	chr5:98125600-98132000	Weak transcription	Stomach Mucosa	stomach
15	chr5:98127400-98131600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:98127600-98131600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:98127600-98131800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:98127600-98131800	Weak transcription	Fetal Kidney	kidney
19	chr5:98127800-98131800	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:98129200-98131600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:98129200-98132200	Weak transcription	Hela-S3	cervix
22	chr5:98129400-98131600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:98129400-98131600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:98129400-98131600	Weak transcription	Left Ventricle	heart
25	chr5:98129400-98131600	Weak transcription	Pancreas	Pancrea
26	chr5:98129400-98131800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:98129400-98131800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:98129400-98131800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:98129400-98132000	Weak transcription	Spleen	Spleen
30	chr5:98129400-98132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:98129400-98132200	Weak transcription	HMEC	breast
32	chr5:98129400-98132600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr5:98129400-98132800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:98129400-98132800	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:98129400-98141200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:98129600-98136000	Weak transcription	Esophagus	oesophagus
37	chr5:98129800-98131800	Weak transcription	Small Intestine	intestine
38	chr5:98130000-98131600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:98130000-98131600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:98130000-98131600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:98130000-98131600	Weak transcription	Brain Anterior Caudate	brain
42	chr5:98130000-98131600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:98130000-98131600	Weak transcription	HepG2	liver
44	chr5:98130000-98131800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:98130000-98131800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:98130000-98131800	Weak transcription	HUVEC	blood vessel
47	chr5:98130000-98132000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr5:98130000-98132200	Weak transcription	Ovary	ovary
49	chr5:98130000-98132200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr5:98130000-98132400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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