Variant report

Variant	rs34495
Chromosome Location	chr5:98265807-98265808
allele	G/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	HEY1	chr5:98265807-98266017	HepG2	liver:	n/a	n/a
2	STAT1	chr5:98263562-98265931	Hela-S3	cervix:	n/a	chr5:98264812-98264824 chr5:98264209-98264221 chr5:98264684-98264696 chr5:98264816-98264828 chr5:98263883-98263895
3	JUND	chr5:98263604-98266054	K562	blood:	n/a	chr5:98264819-98264828 chr5:98264814-98264823 chr5:98264709-98264718 chr5:98264752-98264761 chr5:98263844-98263853 chr5:98263774-98263783 chr5:98264219-98264228 chr5:98264818-98264827
4	TBL1XR1	chr5:98264387-98266187	K562	blood:	n/a	n/a
5	MXI1	chr5:98262891-98265927	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:98262735-98265849	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr5:98262939-98265984	GM19193	blood:	n/a	n/a
8	POLR2A	chr5:98262882-98265836	GM12891	blood:	n/a	n/a
9	POLR2A	chr5:98264398-98266312	A549	lung:	n/a	n/a
10	POLR2A	chr5:98262881-98266666	HepG2	liver:	n/a	n/a
11	MYC	chr5:98263748-98266144	MCF10A-Er-Src	breast:	n/a	chr5:98263904-98263911 chr5:98264544-98264554 chr5:98263903-98263912 chr5:98264754-98264764 chr5:98263849-98263859 chr5:98263901-98263916
12	EGR1	chr5:98264192-98265889	HCT-116	colon:	n/a	chr5:98264836-98264845 chr5:98265424-98265438 chr5:98264835-98264844 chr5:98264818-98264828 chr5:98265225-98265238 chr5:98265480-98265490 chr5:98264819-98264832 chr5:98265424-98265435 chr5:98264226-98264239 chr5:98264362-98264372 chr5:98265087-98265100 chr5:98264709-98264719 chr5:98264721-98264730 chr5:98264509-98264523 chr5:98265324-98265348 chr5:98264360-98264373 chr5:98264285-98264298 chr5:98264541-98264555
13	SIN3AK20	chr5:98263424-98265879	MCF-7	breast:	n/a	n/a
14	POLR2A	chr5:98262802-98266065	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:98262863-98266842	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:98262881-98266708	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:98263568-98265943	K562	blood:	n/a	n/a
18	POLR2A	chr5:98262788-98265865	GM12892	blood:	n/a	n/a
19	POLR2A	chr5:98262824-98265848	GM12892	blood:	n/a	n/a
20	POLR2A	chr5:98262736-98267954	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr5:98263627-98266694	K562	blood:	n/a	n/a
22	HA-E2F1	chr5:98263520-98265951	MCF-7	breast:	n/a	chr5:98263874-98263884 chr5:98264753-98264765 chr5:98264222-98264231 chr5:98263818-98263830 chr5:98265228-98265238 chr5:98264836-98264845
23	POLR2A	chr5:98261911-98271717	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr5:98262744-98270017	GM12891	blood:	n/a	n/a
25	POLR2A	chr5:98262705-98266805	PBDE	blood:	n/a	n/a
26	POLR2A	chr5:98262041-98266821	IMR90	lung:	n/a	n/a
27	POLR2A	chr5:98264112-98265864	U87	brain:	n/a	n/a
28	MXI1	chr5:98264541-98265845	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr5:98262950-98265882	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr5:98264161-98265894	U87	brain:	n/a	n/a
31	JUN	chr5:98264471-98265840	K562	blood:	n/a	chr5:98264819-98264828 chr5:98264814-98264823 chr5:98264709-98264718 chr5:98264752-98264761 chr5:98264818-98264827
32	POLR2A	chr5:98263569-98265999	GM18526	blood:	n/a	n/a
33	POLR2A	chr5:98262906-98266708	K562	blood:	n/a	n/a
34	MXI1	chr5:98264387-98265816	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr5:98262919-98266641	GM12892	blood:	n/a	n/a
36	RFX5	chr5:98264555-98265985	HepG2	liver:	n/a	chr5:98265582-98265595
37	MXI1	chr5:98263642-98265935	HepG2	liver:	n/a	n/a
38	CHD1	chr5:98262479-98266772	IMR90	lung:	n/a	chr5:98263846-98263856 chr5:98265975-98265982 chr5:98264811-98264821 chr5:98264740-98264750
39	SIN3AK20	chr5:98264442-98265809	MCF-7	breast:	n/a	n/a
40	POLR2A	chr5:98262961-98265939	K562	blood:	n/a	n/a
41	POLR2A	chr5:98263724-98265835	HUVEC	blood vessel:	n/a	n/a
42	REST	chr5:98262425-98265892	H1-neurons	neurons:	n/a	chr5:98263595-98263602 chr5:98264406-98264419 chr5:98263123-98263136 chr5:98263593-98263600 chr5:98263120-98263129
43	POLR2A	chr5:98262937-98265874	K562	blood:	n/a	n/a
44	PML	chr5:98262846-98265841	GM12878	blood:	n/a	chr5:98263489-98263497
45	SIN3A	chr5:98262927-98265935	H1-hESC	embryonic stem cell:	n/a	chr5:98264565-98264578
46	RCOR1	chr5:98264345-98266222	K562	blood:	n/a	n/a
47	POLR2A	chr5:98262926-98266642	GM18505	blood:	n/a	n/a
48	POLR2A	chr5:98263024-98266884	HepG2	liver:	n/a	n/a
49	ARID3A	chr5:98264908-98265939	K562	blood:	n/a	n/a
50	POLR2A	chr5:98262941-98266912	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:98262437..98267686-chr5:98287585..98292205,9	K562	blood:
2	chr5:98220770..98224200-chr5:98262773..98266161,4	K562	blood:
3	chr5:90674940..90679357-chr5:98262514..98267275,7	K562	blood:
4	chr5:98265288..98267597-chr5:98314726..98317352,2	K562	blood:
5	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
6	chr5:98265097..98266791-chr5:98309384..98311683,2	K562	blood:
7	chr5:96142600..96144164-chr5:98264927..98267832,2	K562	blood:
8	chr5:98220809..98224769-chr5:98261722..98266325,5	K562	blood:
9	chr5:90677652..90679304-chr5:98264702..98267275,2	K562	blood:
10	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:
11	chr5:90674940..90677586-chr5:98263946..98266440,2	K562	blood:
12	chr5:98265027..98268409-chr5:98365166..98367986,4	K562	blood:
13	chr5:98264902..98266916-chr5:98381565..98384690,3	K562	blood:
14	chr5:98204205..98207501-chr5:98263457..98266267,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGMB-1	chr5:98264838-98266713	NONHSAT102967
2	lnc-RGMB-1	chr5:98264861-98270036	NONHSAT102968
3	lnc-RGMB-1	chr5:98265801-98266772	NONHSAT102970

Variant related genes	Relation type
CHD1	TF binding region
ENSG00000200351	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000153922	Chromatin interaction
ENSG00000164307	Chromatin interaction
ENSG00000241597	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs150991	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs150992	0.83[EUR][1000 genomes]
rs161735	0.93[ASN][1000 genomes]
rs161740	0.93[ASN][1000 genomes]
rs161747	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs161933	0.93[ASN][1000 genomes]
rs161938	0.93[ASN][1000 genomes]
rs161939	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs161941	0.93[ASN][1000 genomes]
rs161942	0.93[ASN][1000 genomes]
rs161948	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs161950	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs161951	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs161952	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs161953	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161954	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs161956	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs162140	0.93[ASN][1000 genomes]
rs162149	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs162150	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2617507	0.97[ASN][1000 genomes]
rs325200	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs325217	0.93[ASN][1000 genomes]
rs326463	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326464	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs326468	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs326469	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs326485	0.93[ASN][1000 genomes]
rs326489	0.93[ASN][1000 genomes]
rs327792	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327793	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs327803	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs327811	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs330419	0.93[ASN][1000 genomes]
rs330421	0.93[ASN][1000 genomes]
rs330422	0.93[ASN][1000 genomes]
rs331926	0.90[ASN][1000 genomes]
rs331929	0.93[ASN][1000 genomes]
rs331931	0.93[ASN][1000 genomes]
rs466340	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692832	0.93[ASN][1000 genomes]
rs751878	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv3405878	chr5:98263077-98265925	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	esv3346760	chr5:98263202-98265950	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34495	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98261200-98266000	Active TSS	Thymus	Thymus
2	chr5:98261600-98266200	Active TSS	Fetal Thymus	thymus
3	chr5:98261800-98266200	Active TSS	K562	blood
4	chr5:98262000-98266000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:98262000-98266000	Active TSS	A549	lung
6	chr5:98262200-98266000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr5:98262400-98266000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:98262400-98266000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr5:98262400-98266000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr5:98262400-98266000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:98262400-98266200	Active TSS	Right Ventricle	heart
12	chr5:98262600-98266000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:98262600-98266000	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr5:98262600-98266000	Active TSS	Colon Smooth Muscle	Colon
15	chr5:98262600-98266000	Active TSS	Fetal Intestine Large	intestine
16	chr5:98262600-98266000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr5:98262600-98266000	Active TSS	HSMM	muscle
18	chr5:98262600-98266200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr5:98262600-98266200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:98262600-98266200	Active TSS	NHLF	lung
21	chr5:98262600-98266400	Active TSS	Psoas Muscle	Psoas
22	chr5:98262600-98266600	Active TSS	Stomach Smooth Muscle	stomach
23	chr5:98262600-98266800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:98262800-98266000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr5:98262800-98266000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:98262800-98266000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:98262800-98266000	Active TSS	Fetal Kidney	kidney
28	chr5:98262800-98266200	Active TSS	Fetal Stomach	stomach
29	chr5:98262800-98266200	Active TSS	HSMMtube	muscle
30	chr5:98262800-98266200	Active TSS	NHDF-Ad	bronchial
31	chr5:98263000-98266000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:98263000-98266000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:98263000-98266000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:98263000-98266000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:98263000-98266000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:98263000-98266000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:98263000-98266000	Active TSS	Muscle Satellite Cultured Cells	--
38	chr5:98263000-98266000	Active TSS	Esophagus	oesophagus
39	chr5:98263000-98266000	Active TSS	Left Ventricle	heart
40	chr5:98263000-98266000	Active TSS	Pancreas	Pancrea
41	chr5:98263000-98266000	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr5:98263000-98266000	Active TSS	Hela-S3	cervix
43	chr5:98263000-98266200	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr5:98263000-98266200	Active TSS	Colonic Mucosa	Colon
45	chr5:98263200-98266000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:98263200-98266000	Active TSS	Aorta	Aorta
47	chr5:98263200-98266200	Active TSS	Fetal Muscle Leg	muscle
48	chr5:98263400-98266400	Active TSS	NH-A	brain
49	chr5:98263600-98266000	Active TSS	Brain Anterior Caudate	brain
50	chr5:98263600-98266200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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