Variant report

Variant	rs2223616
Chromosome Location	chr6:142723002-142723003
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	TCF7L2	chr6:142722565-142723121	HepG2	liver:	n/a	chr6:142722688-142722695

Variant related genes	Relation type
GPR126	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1013902	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17071798	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2064314	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2143390	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294765	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294768	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294770	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294772	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294773	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294774	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34701089	0.84[EUR][1000 genomes]
rs41289839	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140531	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570512	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6913116	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7758750	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7759268	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9321865	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9321871	0.81[EUR][1000 genomes]
rs9373343	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9373345	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376687	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9376689	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9385993	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9385994	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9389988	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9389990	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403379	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9403384	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9484645	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142698600-142733200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:142708000-142734800	Weak transcription	Esophagus	oesophagus
3	chr6:142710200-142733400	Weak transcription	HSMM	muscle
4	chr6:142711400-142725000	Strong transcription	HepG2	liver
5	chr6:142711800-142725200	Strong transcription	Liver	Liver
6	chr6:142712200-142735000	Weak transcription	Fetal Brain Male	brain
7	chr6:142714200-142733200	Weak transcription	HMEC	breast
8	chr6:142717600-142724600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:142717600-142725800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:142718000-142763200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:142718600-142724000	Strong transcription	Placenta	Placenta
12	chr6:142719800-142735400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:142720400-142725000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:142720400-142733200	Weak transcription	NHEK	skin
15	chr6:142720600-142736800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:142721000-142723200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:142721000-142723200	Enhancers	Fetal Intestine Small	intestine
18	chr6:142721600-142723400	Strong transcription	Primary hematopoietic stem cells	blood
19	chr6:142721600-142723800	Genic enhancers	HUVEC	blood vessel
20	chr6:142721600-142749200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:142721800-142725600	Weak transcription	Gastric	stomach
22	chr6:142722000-142728000	Weak transcription	Primary T cells from cord blood	blood
23	chr6:142722000-142743400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:142722200-142728800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:142722200-142731000	Weak transcription	NHLF	lung
26	chr6:142722200-142731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:142722200-142734200	Weak transcription	Hela-S3	cervix
28	chr6:142722400-142723600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:142722400-142725800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:142722400-142725800	Weak transcription	Fetal Lung	lung
31	chr6:142722400-142726000	Weak transcription	Stomach Mucosa	stomach
32	chr6:142722400-142728000	Weak transcription	Small Intestine	intestine
33	chr6:142722400-142728600	Weak transcription	HSMMtube	muscle
34	chr6:142722600-142723200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:142722600-142723600	Weak transcription	A549	lung
36	chr6:142722600-142725800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:142723000-142723400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:142723000-142725800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links