Variant report

Variant	rs161951
Chromosome Location	chr5:98259397-98259398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98257599..98259877-chr5:98263481..98265627,3	MCF-7	breast:
2	chr5:98258735..98261522-chr5:98261609..98263203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1069182	0.86[EUR][1000 genomes]
rs150991	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs150992	0.81[AMR][1000 genomes]
rs161735	0.92[EUR][1000 genomes]
rs161740	0.95[EUR][1000 genomes]
rs161747	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs161933	0.90[EUR][1000 genomes]
rs161938	0.90[EUR][1000 genomes]
rs161939	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs161941	0.89[EUR][1000 genomes]
rs161942	0.89[EUR][1000 genomes]
rs161948	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs161950	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs161952	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs161953	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs161954	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs161956	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs162140	0.90[EUR][1000 genomes]
rs162149	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs162150	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs162473	0.80[EUR][1000 genomes]
rs162611	0.80[EUR][1000 genomes]
rs170734	0.87[EUR][1000 genomes]
rs193072	0.81[EUR][1000 genomes]
rs2617507	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs325200	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs325217	0.89[EUR][1000 genomes]
rs326463	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs326464	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs326468	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs326469	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs326485	0.87[EUR][1000 genomes]
rs326489	0.91[EUR][1000 genomes]
rs327792	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs327793	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs327803	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs330419	0.95[EUR][1000 genomes]
rs330421	0.89[EUR][1000 genomes]
rs330422	0.89[EUR][1000 genomes]
rs331543	0.81[EUR][1000 genomes]
rs331545	0.86[EUR][1000 genomes]
rs331549	0.86[EUR][1000 genomes]
rs331918	0.86[EUR][1000 genomes]
rs331926	0.85[EUR][1000 genomes]
rs331929	0.91[EUR][1000 genomes]
rs331930	0.83[EUR][1000 genomes]
rs331931	0.91[EUR][1000 genomes]
rs34495	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs466340	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs692832	0.95[EUR][1000 genomes]
rs751878	0.85[EUR][1000 genomes]
rs992773	0.86[EUR][1000 genomes]
rs992775	0.86[EUR][1000 genomes]

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
rs161951	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98200000-98263000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:98215000-98263000	Weak transcription	Esophagus	oesophagus
3	chr5:98228400-98259400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:98228400-98263000	Weak transcription	Aorta	Aorta
5	chr5:98235000-98262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:98235200-98261600	Weak transcription	Fetal Kidney	kidney
7	chr5:98235400-98262600	Weak transcription	Fetal Brain Male	brain
8	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:98236600-98261000	Weak transcription	Small Intestine	intestine
10	chr5:98236600-98261600	Weak transcription	Fetal Brain Female	brain
11	chr5:98236600-98263000	Weak transcription	Ovary	ovary
12	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
13	chr5:98240200-98263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:98240800-98263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:98247400-98259600	Weak transcription	Brain Anterior Caudate	brain
16	chr5:98247400-98262600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:98247600-98262200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:98247600-98262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:98248000-98261600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:98249000-98261400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:98249800-98262000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:98251400-98261000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:98252600-98261200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:98253000-98260200	Strong transcription	K562	blood
25	chr5:98253000-98261800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr5:98253200-98259800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:98253200-98261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:98253200-98263000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:98253400-98261000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:98253600-98260200	Strong transcription	Hela-S3	cervix
31	chr5:98253600-98261200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr5:98253600-98261600	Strong transcription	Fetal Intestine Large	intestine
33	chr5:98253600-98261800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:98253800-98260800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:98253800-98262600	Weak transcription	NHLF	lung
36	chr5:98254000-98261000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:98254000-98261200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:98254000-98262200	Strong transcription	Placenta	Placenta
39	chr5:98254200-98260000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:98254200-98262000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:98254600-98260400	Strong transcription	A549	lung
42	chr5:98254600-98261200	Strong transcription	Liver	Liver
43	chr5:98254600-98261400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:98254600-98261600	Strong transcription	HMEC	breast
45	chr5:98254600-98261600	Strong transcription	NH-A	brain
46	chr5:98254600-98261800	Strong transcription	Osteobl	bone
47	chr5:98254600-98262200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:98254800-98260600	Strong transcription	Adipose Nuclei	Adipose
49	chr5:98254800-98261000	Strong transcription	HSMM	muscle
50	chr5:98254800-98261800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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