Variant report

Variant	rs161937
Chromosome Location	chr5:98273862-98273863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:98271988-98274936	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:98272919-98274571	K562	blood:	n/a	n/a
3	POLR2A	chr5:98260830-98273878	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200351	TF binding region
ENSG00000248489	Chromatin interaction
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs109843	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs161949	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2662258	0.87[ASW][hapmap]
rs326488	0.80[EUR][1000 genomes]
rs327786	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs331551	0.87[ASW][hapmap]
rs331917	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs34487	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6860504	0.92[CHD][hapmap]
rs692759	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7718898	0.92[CHD][hapmap]

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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs161937	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266000-98276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:98266000-98276400	Weak transcription	Placenta	Placenta
3	chr5:98266200-98274200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
5	chr5:98266400-98276200	Weak transcription	Fetal Kidney	kidney
6	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
7	chr5:98266800-98274000	Weak transcription	Fetal Lung	lung
8	chr5:98266800-98277000	Weak transcription	HMEC	breast
9	chr5:98266800-98278400	Weak transcription	Hela-S3	cervix
10	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:98267000-98274000	Weak transcription	Adipose Nuclei	Adipose
12	chr5:98267400-98277800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:98269600-98274200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:98269600-98274200	Weak transcription	Thymus	Thymus
15	chr5:98269600-98274400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:98269600-98274600	Weak transcription	Right Atrium	heart
17	chr5:98269800-98274200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:98270000-98275600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:98270200-98274200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:98270200-98276400	Weak transcription	Fetal Thymus	thymus
21	chr5:98270800-98274200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:98270800-98274400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:98271000-98274000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:98271000-98274200	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:98271000-98276000	Weak transcription	Primary T cells from cord blood	blood
26	chr5:98271200-98274000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:98271200-98274000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:98271200-98274000	Weak transcription	NHLF	lung
29	chr5:98271200-98275000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:98271400-98274000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr5:98271400-98274000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr5:98271400-98274200	Weak transcription	Brain Angular Gyrus	brain
33	chr5:98271400-98274200	Weak transcription	Brain Anterior Caudate	brain
34	chr5:98271400-98274600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr5:98271400-98274600	Weak transcription	Left Ventricle	heart
36	chr5:98271600-98274000	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:98271600-98274400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:98271600-98276200	Weak transcription	Primary B cells from cord blood	blood
39	chr5:98272200-98276600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:98272200-98277600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:98272400-98274000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr5:98272400-98275000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr5:98272400-98275200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr5:98272400-98276200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:98272400-98276600	Enhancers	K562	blood
46	chr5:98272400-98278000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:98272600-98275000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr5:98272600-98275000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr5:98272600-98275000	Enhancers	Osteobl	bone
50	chr5:98272600-98275200	Enhancers	Fetal Heart	heart

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