Variant report

Variant	rs12987348
Chromosome Location	chr2:153354784-153354785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153353996..153356046-chr2:153357031..153359533,2	K562	blood:
2	chr2:153345928..153348906-chr2:153354040..153356962,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12104452	1.00[EUR][1000 genomes]
rs12989840	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs12991474	1.00[EUR][1000 genomes]
rs12993239	1.00[EUR][1000 genomes]
rs12999189	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011850	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs13018434	1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021931	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs13023943	0.91[YRI][hapmap]
rs13027160	1.00[EUR][1000 genomes]
rs13027356	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs13029667	1.00[EUR][1000 genomes]
rs13034458	1.00[EUR][1000 genomes]
rs16831151	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs16831161	1.00[ASN][1000 genomes]
rs34300140	1.00[EUR][1000 genomes]
rs34332337	1.00[EUR][1000 genomes]
rs34416306	1.00[EUR][1000 genomes]
rs34457645	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34504342	1.00[EUR][1000 genomes]
rs34722196	1.00[EUR][1000 genomes]
rs35199259	1.00[EUR][1000 genomes]
rs35472114	1.00[EUR][1000 genomes]
rs35804350	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36108117	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664120	1.00[CHB][hapmap]
rs59579926	0.89[ASN][1000 genomes]
rs6434046	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs6731516	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs6745613	1.00[EUR][1000 genomes]
rs71417227	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71417229	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73016010	1.00[EUR][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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153342600-153355800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:153343000-153360600	Enhancers	Brain Anterior Caudate	brain
3	chr2:153348600-153357200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:153348800-153370200	Weak transcription	Aorta	Aorta
5	chr2:153350400-153357400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:153350800-153355800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:153350800-153357000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:153350800-153360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:153351000-153355600	Weak transcription	Fetal Stomach	stomach
10	chr2:153351200-153355400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:153351400-153355200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:153351400-153355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:153351400-153357600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:153351400-153361000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:153351600-153355200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:153351600-153359600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:153351800-153355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:153352000-153359800	Enhancers	Brain Substantia Nigra	brain
19	chr2:153352200-153356000	Enhancers	Brain Hippocampus Middle	brain
20	chr2:153352400-153355200	Weak transcription	Fetal Kidney	kidney
21	chr2:153353400-153356400	Enhancers	HepG2	liver
22	chr2:153353600-153354800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr2:153353600-153355600	Weak transcription	Fetal Brain Male	brain
24	chr2:153353600-153357000	Enhancers	Hela-S3	cervix
25	chr2:153353800-153354800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:153353800-153356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:153354000-153354800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:153354000-153354800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:153354000-153354800	Enhancers	Osteobl	bone
30	chr2:153354000-153355800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:153354000-153356000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:153354200-153354800	Enhancers	Ovary	ovary
33	chr2:153354200-153354800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr2:153354200-153354800	Flanking Active TSS	GM12878-XiMat	blood
35	chr2:153354200-153354800	Enhancers	HMEC	breast
36	chr2:153354200-153354800	Enhancers	NH-A	brain
37	chr2:153354200-153355000	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:153354200-153357200	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:153354200-153357200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:153354200-153357200	Enhancers	Fetal Intestine Large	intestine
41	chr2:153354200-153357200	Enhancers	Fetal Intestine Small	intestine
42	chr2:153354200-153357200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:153354200-153358200	Enhancers	Adipose Nuclei	Adipose
44	chr2:153354200-153358800	Enhancers	Brain Angular Gyrus	brain
45	chr2:153354200-153360000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:153354400-153354800	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr2:153354400-153354800	Enhancers	K562	blood
48	chr2:153354400-153355400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:153354400-153355400	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr2:153354400-153356200	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links