Variant report

Variant	rs161950
Chromosome Location	chr5:98260237-98260238
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	chr5:98259484-98260330	K562	blood:	n/a	n/a

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

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

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1069182	0.86[EUR][1000 genomes]
rs11948998	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs11956636	1.00[CHD][hapmap]
rs150991	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs150992	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs151102	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs161731	0.83[CEU][hapmap]
rs161735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161740	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161747	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161933	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161938	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161939	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161941	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161942	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161948	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs161951	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs161952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs161953	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161956	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs162140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162150	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162473	0.80[EUR][1000 genomes]
rs162611	0.80[EUR][1000 genomes]
rs170734	0.87[EUR][1000 genomes]
rs17166428	1.00[CHD][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap]
rs193072	0.81[EUR][1000 genomes]
rs2545735	0.86[JPT][hapmap]
rs2617507	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs325200	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325217	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs325220	0.83[CEU][hapmap]
rs326463	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326464	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326468	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326469	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326480	0.82[CEU][hapmap]
rs326485	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326489	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs327792	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327793	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327803	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327811	0.95[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs330419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][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];0.90[ASN][1000 genomes]
rs331929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331930	0.83[EUR][1000 genomes]
rs331931	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34495	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs40075	0.83[CEU][hapmap]
rs466340	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467728	0.82[CEU][hapmap]
rs6866629	0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs692832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs727637	1.00[CHD][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap]
rs73776028	0.81[AFR][1000 genomes]
rs751878	0.85[EUR][1000 genomes];0.87[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs161950	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs161950	CHD1	cis	brain	BrainEAC

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	chr5:98228400-98263000	Weak transcription	Aorta	Aorta
4	chr5:98235000-98262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:98235200-98261600	Weak transcription	Fetal Kidney	kidney
6	chr5:98235400-98262600	Weak transcription	Fetal Brain Male	brain
7	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:98236600-98261000	Weak transcription	Small Intestine	intestine
9	chr5:98236600-98261600	Weak transcription	Fetal Brain Female	brain
10	chr5:98236600-98263000	Weak transcription	Ovary	ovary
11	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:98240200-98263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:98240800-98263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:98247400-98262600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:98247600-98262200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:98247600-98262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:98248000-98261600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:98249000-98261400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:98249800-98262000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:98251400-98261000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:98252600-98261200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:98253000-98261800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr5:98253200-98261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:98253200-98263000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:98253400-98261000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:98253600-98261200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr5:98253600-98261600	Strong transcription	Fetal Intestine Large	intestine
28	chr5:98253600-98261800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:98253800-98260800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:98253800-98262600	Weak transcription	NHLF	lung
31	chr5:98254000-98261000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:98254000-98261200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:98254000-98262200	Strong transcription	Placenta	Placenta
34	chr5:98254200-98262000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:98254600-98260400	Strong transcription	A549	lung
36	chr5:98254600-98261200	Strong transcription	Liver	Liver
37	chr5:98254600-98261400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:98254600-98261600	Strong transcription	HMEC	breast
39	chr5:98254600-98261600	Strong transcription	NH-A	brain
40	chr5:98254600-98261800	Strong transcription	Osteobl	bone
41	chr5:98254600-98262200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:98254800-98260600	Strong transcription	Adipose Nuclei	Adipose
43	chr5:98254800-98261000	Strong transcription	HSMM	muscle
44	chr5:98254800-98261800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:98255000-98261600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr5:98255200-98261600	Strong transcription	Fetal Muscle Leg	muscle
47	chr5:98255200-98261800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:98255200-98263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr5:98255400-98261600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:98255400-98261600	Strong transcription	Duodenum Mucosa	Duodenum

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