Variant report

Variant	rs11898252
Chromosome Location	chr2:134179065-134179066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134178712..134179890-chr2:134318289..134319234,5	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10165601	0.89[ASN][1000 genomes]
rs10171473	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10175744	0.89[ASN][1000 genomes]
rs10180047	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10182656	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10184630	0.95[ASN][1000 genomes]
rs10191826	0.85[ASN][1000 genomes]
rs10193087	0.95[ASN][1000 genomes]
rs10193730	0.98[ASN][1000 genomes]
rs10196395	0.98[ASN][1000 genomes]
rs10204436	0.98[ASN][1000 genomes]
rs10204527	0.98[ASN][1000 genomes]
rs10206474	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10928451	0.85[ASN][1000 genomes]
rs11890293	0.88[ASN][1000 genomes]
rs12327930	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12328723	0.88[ASN][1000 genomes]
rs12328976	0.80[ASN][1000 genomes]
rs13392963	0.86[ASN][1000 genomes]
rs13396831	0.97[ASN][1000 genomes]
rs13396930	0.92[ASN][1000 genomes]
rs13400561	0.83[ASN][1000 genomes]
rs13400743	0.83[ASN][1000 genomes]
rs13406057	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13406354	0.84[ASN][1000 genomes]
rs13407205	0.89[ASN][1000 genomes]
rs13407503	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13408835	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13411233	0.88[ASN][1000 genomes]
rs13412956	0.97[ASN][1000 genomes]
rs13421761	0.97[ASN][1000 genomes]
rs13426157	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13426681	0.92[ASN][1000 genomes]
rs1346776	0.82[ASN][1000 genomes]
rs1369509	0.86[ASN][1000 genomes]
rs1369510	0.97[ASN][1000 genomes]
rs1430166	0.85[ASN][1000 genomes]
rs1430167	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1430168	0.91[ASN][1000 genomes]
rs1435554	0.88[ASN][1000 genomes]
rs1435563	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435564	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1435565	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1435566	0.91[ASN][1000 genomes]
rs1561018	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16824299	0.85[ASN][1000 genomes]
rs16824301	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824303	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824511	0.97[ASN][1000 genomes]
rs16824573	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745593	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17745851	0.97[ASN][1000 genomes]
rs17802295	0.95[ASN][1000 genomes]
rs1898008	0.95[ASN][1000 genomes]
rs2115864	0.83[ASN][1000 genomes]
rs2164326	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289075	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2304404	0.88[ASN][1000 genomes]
rs28445548	0.85[ASN][1000 genomes]
rs4588241	0.86[ASN][1000 genomes]
rs55788182	0.92[ASN][1000 genomes]
rs56410092	0.85[ASN][1000 genomes]
rs58489491	0.88[ASN][1000 genomes]
rs62177662	0.88[ASN][1000 genomes]
rs62177669	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62177672	0.97[ASN][1000 genomes]
rs62180011	0.83[ASN][1000 genomes]
rs62180012	0.83[ASN][1000 genomes]
rs62180016	0.91[ASN][1000 genomes]
rs62180017	0.88[ASN][1000 genomes]
rs7573164	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9287426	0.95[ASN][1000 genomes]
rs990476	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834384	chr2:134005229-134188648	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134165400-134179200	Weak transcription	Esophagus	oesophagus
2	chr2:134171400-134183800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:134173200-134179200	Weak transcription	Left Ventricle	heart
4	chr2:134173200-134179200	Weak transcription	Right Atrium	heart
5	chr2:134174200-134182800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:134175200-134182800	Weak transcription	NHDF-Ad	bronchial
7	chr2:134175400-134179200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:134176200-134179200	Weak transcription	Brain Anterior Caudate	brain
9	chr2:134176800-134179200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:134177000-134179200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:134177800-134180200	Enhancers	Fetal Intestine Small	intestine
12	chr2:134177800-134181400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:134178200-134180000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:134178200-134180600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:134178200-134181200	Enhancers	NHEK	skin
16	chr2:134178200-134185200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:134178400-134179400	Active TSS	Colonic Mucosa	Colon
18	chr2:134178400-134181000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:134178400-134181000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:134178400-134181000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:134178400-134183200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:134178600-134179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:134178600-134179200	Enhancers	Fetal Lung	lung
24	chr2:134178600-134179800	Enhancers	Fetal Kidney	kidney
25	chr2:134178600-134180000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr2:134178600-134180000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr2:134178600-134180800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:134178600-134181000	Enhancers	Fetal Brain Female	brain
29	chr2:134178600-134183600	Enhancers	Brain Substantia Nigra	brain
30	chr2:134178800-134179200	Active TSS	A549	lung
31	chr2:134178800-134179400	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr2:134178800-134179400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr2:134178800-134179600	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:134178800-134180400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:134178800-134180800	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:134178800-134180800	Enhancers	Fetal Heart	heart
37	chr2:134178800-134181000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr2:134178800-134181000	Enhancers	Brain Hippocampus Middle	brain
39	chr2:134178800-134181000	Enhancers	Fetal Brain Male	brain
40	chr2:134178800-134183600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr2:134179000-134179200	Enhancers	HMEC	breast
42	chr2:134179000-134179400	Flanking Active TSS	Liver	Liver
43	chr2:134179000-134179400	Enhancers	Brain Angular Gyrus	brain
44	chr2:134179000-134179400	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr2:134179000-134179600	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:134179000-134179800	Enhancers	NH-A	brain
47	chr2:134179000-134180000	Enhancers	Pancreas	Pancrea
48	chr2:134179000-134180200	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr2:134179000-134180400	Enhancers	Hela-S3	cervix
50	chr2:134179000-134180800	Enhancers	Stomach Mucosa	stomach

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