Variant report

Variant	rs161739
Chromosome Location	chr5:98204569-98204570
allele	C/T
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	chr5:98204455-98204669	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:98204149-98204980	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98204205..98207501-chr5:98263457..98266267,3	MCF-7	breast:

Variant related genes	Relation type
CHD1	TF binding region
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs150935	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152034	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161729	0.87[ASW][hapmap];1.00[YRI][hapmap]
rs161732	0.87[ASW][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs161734	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161735	0.88[JPT][hapmap]
rs161736	0.88[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]
rs161737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161744	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161745	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161746	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161749	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161750	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161940	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161945	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161957	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545680	1.00[YRI][hapmap]
rs2545733	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545734	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2545735	0.86[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]
rs2545736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545737	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545738	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545739	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545740	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578576	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578577	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617514	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662256	0.83[YRI][hapmap]
rs325195	1.00[YRI][hapmap]
rs325199	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325203	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][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]
rs325204	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][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]
rs325208	0.88[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];0.90[ASN][1000 genomes]
rs325209	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325214	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326481	0.83[YRI][hapmap]
rs326482	0.83[YRI][hapmap]
rs326487	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331541	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs331542	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs331544	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs331548	0.90[EUR][1000 genomes]
rs331927	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331928	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34498	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs4583911	1.00[YRI][hapmap]
rs469519	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719562	0.83[YRI][hapmap]
rs819230	1.00[YRI][hapmap]
rs992774	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs161739	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98180200-98213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:98182600-98205000	Weak transcription	NHEK	skin
3	chr5:98186200-98213400	Weak transcription	Esophagus	oesophagus
4	chr5:98188400-98247000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:98189200-98205000	Weak transcription	NHLF	lung
6	chr5:98189400-98205800	Weak transcription	Fetal Heart	heart
7	chr5:98189400-98227400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:98189600-98213800	Weak transcription	HSMMtube	muscle
9	chr5:98189600-98215400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:98189600-98241000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:98189800-98241000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:98189800-98241400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:98189800-98241400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:98189800-98241800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:98190000-98240600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:98190000-98240800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr5:98190000-98240800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:98190200-98240600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:98190200-98240600	Strong transcription	Liver	Liver
20	chr5:98190200-98241000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr5:98190400-98205400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:98190400-98212400	Weak transcription	Small Intestine	intestine
23	chr5:98190400-98213200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:98190400-98214600	Weak transcription	Aorta	Aorta
25	chr5:98190400-98224200	Strong transcription	Placenta	Placenta
26	chr5:98190400-98234600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:98190400-98238200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:98190400-98238800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:98190400-98240000	Weak transcription	Stomach Mucosa	stomach
30	chr5:98190400-98240400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:98190400-98240600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr5:98190400-98240800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr5:98190400-98241200	Strong transcription	Fetal Thymus	thymus
34	chr5:98190400-98243800	Strong transcription	Dnd41	blood
35	chr5:98190600-98209400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:98190600-98240600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:98190600-98240800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:98190600-98240800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:98190600-98241000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:98190800-98209800	Strong transcription	Adipose Nuclei	Adipose
41	chr5:98190800-98216200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:98190800-98226000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:98190800-98240000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:98191000-98225600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:98191000-98240800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr5:98191400-98213600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:98192000-98204800	Weak transcription	Colon Smooth Muscle	Colon
48	chr5:98192200-98214600	Weak transcription	Brain Angular Gyrus	brain
49	chr5:98192400-98206000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:98193600-98219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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