Variant report

Variant	rs2111459
Chromosome Location	chr2:172174263-172174264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172163945..172166501-chr2:172172840..172175232,2	MCF-7	breast:
2	chr2:172172770..172175059-chr2:172182962..172185953,2	K562	blood:
3	chr2:172172855..172175323-chr2:172409152..172411417,2	K562	blood:
4	chr2:172172261..172175023-chr2:172288680..172291417,3	K562	blood:

Variant related genes	Relation type
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10454741	0.86[AMR][1000 genomes]
rs11674632	0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11677795	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11679835	0.85[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs11687454	0.92[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11691073	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11694321	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11893310	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11902733	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12105780	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12989392	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12989938	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12995219	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12998320	1.00[GIH][hapmap];0.81[MEX][hapmap]
rs13000846	0.93[GIH][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13002817	0.92[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13002867	0.86[AMR][1000 genomes]
rs13003130	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13023287	0.88[AMR][1000 genomes]
rs13023973	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13031794	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13398989	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2356707	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34096402	0.86[AMR][1000 genomes]
rs36140780	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4668380	0.89[CEU][hapmap]
rs67077741	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6722670	0.85[ASW][hapmap];0.92[GIH][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7592018	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2111459	METTL8	Cis_1M	lymphoblastoid	RTeQTL
rs2111459	LASS6	cis	parietal	SCAN
rs2111459	CDCA7	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172163800-172181400	Weak transcription	Gastric	stomach
2	chr2:172165600-172179400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:172168800-172174800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:172169000-172174800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:172169200-172175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:172169200-172175000	Weak transcription	Adipose Nuclei	Adipose
7	chr2:172169200-172175600	Weak transcription	HepG2	liver
8	chr2:172169200-172178800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:172169200-172182400	Weak transcription	Aorta	Aorta
10	chr2:172169200-172193400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:172169400-172179400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:172169600-172175200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:172169600-172179400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:172169800-172177200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:172169800-172181200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:172169800-172183200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:172170200-172192800	Weak transcription	Fetal Intestine Large	intestine
18	chr2:172170600-172178000	Weak transcription	Dnd41	blood
19	chr2:172170800-172175600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:172170800-172177800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:172171000-172175200	Weak transcription	Primary T cells from cord blood	blood
22	chr2:172171000-172177400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr2:172171200-172175000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr2:172171200-172175200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr2:172171200-172175200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:172171200-172178000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:172171400-172190800	Weak transcription	Esophagus	oesophagus
28	chr2:172171600-172176000	Weak transcription	K562	blood
29	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
30	chr2:172172000-172177600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:172172000-172177800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:172172200-172175400	Enhancers	Fetal Muscle Leg	muscle
33	chr2:172172400-172175000	Enhancers	Brain Germinal Matrix	brain
34	chr2:172172400-172175200	Enhancers	Colon Smooth Muscle	Colon
35	chr2:172172400-172176200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:172172400-172177200	Enhancers	Rectal Smooth Muscle	rectum
37	chr2:172172400-172177400	Enhancers	Brain Angular Gyrus	brain
38	chr2:172172400-172177400	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:172172400-172177800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:172172400-172178000	Enhancers	Fetal Brain Male	brain
41	chr2:172172600-172175800	Weak transcription	HMEC	breast
42	chr2:172172600-172177600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr2:172172600-172177600	Weak transcription	Left Ventricle	heart
44	chr2:172172600-172179800	Weak transcription	Fetal Thymus	thymus
45	chr2:172172600-172190600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:172172800-172190600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:172173000-172182200	Weak transcription	Liver	Liver
49	chr2:172173200-172175000	Weak transcription	Fetal Stomach	stomach
50	chr2:172173400-172174400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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