Variant report

Variant	rs17198787
Chromosome Location	chr2:190029162-190029163
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190016341..190018052-chr2:190028651..190030939,2	MCF-7	breast:
2	chr2:190027832..190030639-chr2:190032693..190035632,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10497699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931402	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10931406	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10931410	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11675295	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11676812	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11677073	0.85[ASN][1000 genomes]
rs11678388	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11681937	0.85[ASN][1000 genomes]
rs11684417	0.85[ASN][1000 genomes]
rs11684869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11687908	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11690774	0.95[EUR][1000 genomes]
rs11693810	0.85[ASN][1000 genomes]
rs11695837	0.88[EUR][1000 genomes]
rs12472232	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1515873	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1515875	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1519185	0.85[ASN][1000 genomes]
rs1520862	0.85[ASN][1000 genomes]
rs17198773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17198780	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17198815	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17198829	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17270952	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17270966	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17270973	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17270987	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17271008	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17271015	0.85[ASN][1000 genomes]
rs1996576	0.85[ASN][1000 genomes]
rs2683013	0.85[ASN][1000 genomes]
rs2683014	0.85[ASN][1000 genomes]
rs35598715	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55726777	0.81[ASN][1000 genomes]
rs55851872	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56252219	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56381644	0.81[EUR][1000 genomes]
rs59031473	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61130121	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61528955	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62182060	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62182061	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62182066	0.85[ASN][1000 genomes]
rs62182068	0.85[ASN][1000 genomes]
rs62182069	0.85[ASN][1000 genomes]
rs62182415	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182420	0.80[EUR][1000 genomes]
rs62182421	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182454	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182457	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182458	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182459	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183794	0.97[ASN][1000 genomes]
rs62183841	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183844	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183845	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183846	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62183847	0.85[EUR][1000 genomes]
rs62183848	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72908368	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72908382	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72910347	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72910360	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72912280	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72912286	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72914141	0.85[ASN][1000 genomes]
rs7564429	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7586853	0.90[EUR][1000 genomes];0.91[ASN][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190018800-190029600	Weak transcription	Ovary	ovary
2	chr2:190019600-190040000	Weak transcription	Fetal Intestine Small	intestine
3	chr2:190021000-190031400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:190026600-190029200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:190026600-190029600	Enhancers	HSMMtube	muscle
6	chr2:190026600-190030200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:190026600-190032000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:190026800-190029200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:190026800-190029800	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:190026800-190030800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:190027000-190029400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:190027200-190030800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:190027400-190029200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:190027600-190029800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:190027600-190032000	Enhancers	Fetal Lung	lung
16	chr2:190027800-190029200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:190027800-190029400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:190027800-190031400	Enhancers	NH-A	brain
19	chr2:190028000-190029400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:190028000-190029600	Enhancers	Fetal Heart	heart
21	chr2:190028000-190030800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:190028000-190032800	Enhancers	NHLF	lung
23	chr2:190028200-190029200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr2:190028200-190030000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:190028200-190030400	Enhancers	Hela-S3	cervix
26	chr2:190028200-190030600	Enhancers	Adipose Nuclei	Adipose
27	chr2:190028400-190029200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:190028400-190029200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:190028400-190029200	Flanking Active TSS	A549	lung
30	chr2:190028400-190029400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr2:190028400-190029400	Enhancers	Fetal Kidney	kidney
32	chr2:190028400-190029600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:190028400-190030000	Enhancers	HUVEC	blood vessel
34	chr2:190028400-190030600	Enhancers	Fetal Stomach	stomach
35	chr2:190028400-190033800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:190028600-190030800	Enhancers	NHDF-Ad	bronchial
37	chr2:190028800-190029600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:190028800-190029800	Enhancers	HMEC	breast
39	chr2:190028800-190030000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:190028800-190030000	Enhancers	HSMM	muscle
41	chr2:190028800-190030200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:190028800-190030200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:190028800-190034200	Enhancers	Liver	Liver
44	chr2:190029000-190029200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:190029000-190029600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:190029000-190029600	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:190029000-190029600	Weak transcription	Psoas Muscle	Psoas
48	chr2:190029000-190029600	Enhancers	Osteobl	bone
49	chr2:190029000-190030200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:190029000-190030600	Weak transcription	Colon Smooth Muscle	Colon

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