Variant report

Variant	rs62088909
Chromosome Location	chr18:9611214-9611215
allele	C/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	chr18:9610987-9611447	K562	blood:	n/a	n/a
2	POLR2A	chr18:9611134-9611342	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9610312..9611854-chr18:9611926..9614343,2	MCF-7	breast:
2	chr18:9598014..9601741-chr18:9607589..9612497,6	MCF-7	breast:
3	chr18:9611182..9615699-chr18:9705314..9711194,13	MCF-7	breast:
4	chr18:9610247..9612763-chr18:9683592..9685519,2	K562	blood:

Variant related genes	Relation type
ENSG00000263627	TF binding region
ENSG00000154845	Chromatin interaction
ENSG00000168461	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs61746389	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61749090	0.85[EUR][1000 genomes]
rs61749091	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62080294	0.85[AMR][1000 genomes]
rs62080298	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62080299	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62080302	0.81[EUR][1000 genomes]
rs62080303	0.81[EUR][1000 genomes]
rs62087423	0.80[EUR][1000 genomes]
rs62087424	0.97[EUR][1000 genomes]
rs62087455	0.97[EUR][1000 genomes]
rs62087457	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62087458	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62088862	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62088863	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62088865	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62088866	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62088867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62088869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62088874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62088882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62088910	0.95[AMR][1000 genomes]
rs62088911	0.83[EUR][1000 genomes]
rs62088912	0.81[EUR][1000 genomes]
rs62088913	0.81[EUR][1000 genomes]
rs62088914	0.81[EUR][1000 genomes]
rs62088915	0.85[EUR][1000 genomes]
rs62088917	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62088918	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7236182	0.81[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	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62088909	RALBP1	cis	Whole Blood	GTEx
rs62088909	RP11-692N5.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr18:9594200-9613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:9595200-9612000	Weak transcription	Esophagus	oesophagus
6	chr18:9597400-9613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:9598000-9612600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr18:9601800-9612200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr18:9604800-9612200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr18:9604800-9612400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr18:9605600-9611600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:9607200-9613400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr18:9608000-9611600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr18:9608200-9613600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr18:9608600-9611400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr18:9609000-9612200	Weak transcription	Fetal Kidney	kidney
17	chr18:9609000-9612400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr18:9609200-9612200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr18:9609400-9612000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr18:9609400-9612000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr18:9609400-9612400	Weak transcription	Aorta	Aorta
22	chr18:9609400-9612600	Weak transcription	Brain Angular Gyrus	brain
23	chr18:9609400-9612800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr18:9609400-9613600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr18:9609600-9611400	Genic enhancers	NHEK	skin
26	chr18:9609600-9612000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr18:9609600-9612200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr18:9609600-9612200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr18:9609600-9612200	Weak transcription	Brain Substantia Nigra	brain
30	chr18:9609600-9612200	Weak transcription	Left Ventricle	heart
31	chr18:9609600-9612200	Weak transcription	Small Intestine	intestine
32	chr18:9609600-9612200	Strong transcription	HSMM	muscle
33	chr18:9609600-9612400	Weak transcription	Ovary	ovary
34	chr18:9609600-9612400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr18:9609600-9612400	Weak transcription	Right Atrium	heart
36	chr18:9609600-9612400	Weak transcription	Right Ventricle	heart
37	chr18:9609600-9612600	Weak transcription	Primary T cells from cord blood	blood
38	chr18:9609600-9613000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr18:9609600-9613200	Weak transcription	Thymus	Thymus
40	chr18:9609600-9613400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr18:9609800-9612200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr18:9609800-9612200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr18:9609800-9613000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr18:9610000-9612400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr18:9610200-9612200	Genic enhancers	K562	blood
46	chr18:9610400-9611400	Strong transcription	Fetal Stomach	stomach
47	chr18:9610400-9611600	Strong transcription	Fetal Intestine Small	intestine
48	chr18:9610400-9611600	Genic enhancers	Fetal Muscle Leg	muscle
49	chr18:9610400-9612000	Genic enhancers	HUVEC	blood vessel
50	chr18:9610400-9612200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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