Variant report

Variant	rs10181040
Chromosome Location	chr2:149009980-149009981
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:56707881..56710421-chr2:149007960..149010940,2	K562	blood:
2	chr17:56707748..56709669-chr2:149007960..149010940,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10084286	1.00[AMR][1000 genomes]
rs10168627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10169814	1.00[AMR][1000 genomes]
rs10172107	0.89[AFR][1000 genomes]
rs10172459	0.89[AFR][1000 genomes]
rs10172623	1.00[AMR][1000 genomes]
rs10172638	1.00[AMR][1000 genomes]
rs10174213	1.00[AMR][1000 genomes]
rs10174231	1.00[AMR][1000 genomes]
rs10174899	0.89[AFR][1000 genomes]
rs10175126	0.89[AFR][1000 genomes]
rs10179991	0.89[AFR][1000 genomes]
rs10180813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181462	0.89[AFR][1000 genomes]
rs10186976	0.89[AFR][1000 genomes]
rs10187257	0.89[AFR][1000 genomes]
rs10189852	0.89[AFR][1000 genomes]
rs10191867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10195846	1.00[AMR][1000 genomes]
rs10197288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10199100	0.89[AFR][1000 genomes]
rs10199661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10206286	0.89[AFR][1000 genomes]
rs10211580	1.00[AMR][1000 genomes]
rs13385606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13385697	0.89[AFR][1000 genomes]
rs13386143	1.00[AMR][1000 genomes]
rs13387197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13395948	1.00[AMR][1000 genomes]
rs13396012	1.00[AMR][1000 genomes]
rs13397712	0.89[AFR][1000 genomes]
rs13399551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401666	1.00[AMR][1000 genomes]
rs13403934	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404496	1.00[AMR][1000 genomes]
rs13404809	1.00[AMR][1000 genomes]
rs13417167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13420788	0.89[AFR][1000 genomes]
rs13422826	0.89[AFR][1000 genomes]
rs13426081	0.89[AFR][1000 genomes]
rs13426527	1.00[AMR][1000 genomes]
rs28405957	0.89[AFR][1000 genomes]
rs28594070	0.89[AFR][1000 genomes]
rs28647742	0.93[AFR][1000 genomes];1.00[AMR][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	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148984400-149011800	Weak transcription	Gastric	stomach
2	chr2:148984800-149011800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:148985400-149011200	Weak transcription	Pancreas	Pancrea
4	chr2:148986800-149011600	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:148990200-149011400	Weak transcription	Spleen	Spleen
6	chr2:148994800-149016600	Weak transcription	Fetal Brain Male	brain
7	chr2:148995000-149019800	Weak transcription	Aorta	Aorta
8	chr2:148995000-149030800	Weak transcription	Left Ventricle	heart
9	chr2:148995200-149011000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:148995200-149011400	Weak transcription	Placenta	Placenta
11	chr2:148995400-149010400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:148995400-149011200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:148995400-149011200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:148995400-149011400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:148995400-149013400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:148995400-149015200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:148995800-149010800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:148996400-149010000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:148996400-149011400	Weak transcription	Adipose Nuclei	Adipose
20	chr2:148996400-149030400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:148997000-149012000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:148997400-149010400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:148997400-149011000	Weak transcription	Fetal Kidney	kidney
24	chr2:148997800-149011400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:148998600-149011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:148999400-149016400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:149002600-149015600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:149002800-149012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:149002800-149012000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:149002800-149016600	Weak transcription	NHLF	lung
31	chr2:149003000-149011200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:149003000-149011400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:149003200-149011200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:149003800-149011800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:149006000-149011200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:149007000-149011400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:149007400-149011000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:149008000-149010400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:149008000-149013800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:149008200-149010400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:149008200-149011400	Weak transcription	Right Ventricle	heart
42	chr2:149009200-149016600	ZNF genes & repeats	GM12878-XiMat	blood
43	chr2:149009400-149010000	Enhancers	HepG2	liver
44	chr2:149009400-149012200	ZNF genes & repeats	Primary T cells from cord blood	blood
45	chr2:149009400-149017600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:149009600-149010200	ZNF genes & repeats	Fetal Stomach	stomach
47	chr2:149009600-149010600	Strong transcription	Ovary	ovary
48	chr2:149009600-149012000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
49	chr2:149009600-149017600	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr2:149009800-149010000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links