Variant report

Variant	rs2668235
Chromosome Location	chr12:121665334-121665335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121664342..121666780-chr12:121734216..121737104,3	MCF-7	breast:
2	chr12:121664973..121666491-chr12:121668545..121670113,2	K562	blood:
3	chr12:121640765..121641418-chr12:121664955..121665790,2	MCF-7	breast:
4	chr12:121654852..121658533-chr12:121664523..121668061,3	K562	blood:
5	chr12:121659173..121660678-chr12:121664466..121666483,2	K562	blood:
6	chr12:121659123..121660673-chr12:121663523..121665966,2	K562	blood:
7	chr12:121640762..121641344-chr12:121664895..121665592,2	MCF-7	breast:
8	chr12:121660136..121663309-chr12:121663557..121666409,5	MCF-7	breast:
9	chr12:121646468..121649464-chr12:121663700..121666381,2	K562	blood:
10	chr12:121646834..121652613-chr12:121661734..121667006,9	MCF-7	breast:
11	chr12:121662095..121663648-chr12:121665319..121667911,2	K562	blood:
12	chr12:121664133..121666878-chr12:121668504..121670264,2	K562	blood:
13	chr12:121521823..121524170-chr12:121665223..121666931,2	MCF-7	breast:
14	chr12:121613534..121614299-chr12:121664938..121665536,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135124	Chromatin interaction
ENSG00000110931	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10774587	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849855	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849856	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849858	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065479	0.82[AMR][1000 genomes]
rs11065486	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1169720	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1169727	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1180051	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182945	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1629287	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653622	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1653623	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1718117	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071271	0.90[ASN][1000 genomes]
rs2393849	0.95[ASN][1000 genomes]
rs2393850	0.92[ASN][1000 genomes]
rs25643	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2567978	0.83[ASN][1000 genomes]
rs2567980	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2567993	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2567994	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668252	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2686362	0.85[AMR][1000 genomes]
rs2686363	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686387	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2686388	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2942063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58232824	0.95[ASN][1000 genomes]
rs6489799	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs725135	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298368	0.92[ASN][1000 genomes]
rs930186	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930187	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2668235	CAMKK2	Cis_1M	lymphoblastoid	RTeQTL
rs2668235	ENSG00000135124	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121648800-121666600	Weak transcription	Ovary	ovary
2	chr12:121649000-121666600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:121649000-121675800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:121649000-121676200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:121649000-121676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:121649000-121676600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:121649400-121680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:121652400-121675600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:121653200-121666400	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:121653200-121675600	Weak transcription	HSMMtube	muscle
11	chr12:121653200-121698800	Weak transcription	Fetal Heart	heart
12	chr12:121653400-121673600	Weak transcription	Osteobl	bone
13	chr12:121653400-121677600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:121653400-121678600	Weak transcription	Right Atrium	heart
15	chr12:121653600-121670200	Weak transcription	NHDF-Ad	bronchial
16	chr12:121654800-121675200	Strong transcription	Fetal Stomach	stomach
17	chr12:121655200-121678000	Weak transcription	Fetal Kidney	kidney
18	chr12:121655400-121667400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:121655400-121667800	Weak transcription	A549	lung
20	chr12:121656000-121666600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:121656600-121666600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:121657000-121671600	Weak transcription	HUVEC	blood vessel
23	chr12:121657000-121676200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:121657200-121666400	Weak transcription	Brain Substantia Nigra	brain
25	chr12:121658200-121673600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:121658800-121671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:121659400-121667600	Strong transcription	Fetal Muscle Leg	muscle
28	chr12:121660400-121665600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:121660600-121665400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:121660600-121665600	Enhancers	Primary T cells from cord blood	blood
31	chr12:121660600-121665600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:121660600-121665600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:121660600-121666000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr12:121660800-121665600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr12:121660800-121667600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:121661000-121666600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:121661600-121666600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:121661600-121666600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:121661600-121667600	Weak transcription	Hela-S3	cervix
40	chr12:121661600-121667800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr12:121661600-121675800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:121661600-121675800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:121661800-121665800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr12:121661800-121665800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:121661800-121666400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:121661800-121666400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:121661800-121666600	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:121661800-121666600	Weak transcription	Esophagus	oesophagus
49	chr12:121661800-121666600	Weak transcription	Right Ventricle	heart
50	chr12:121661800-121671000	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links