Variant report

Variant	rs17198780
Chromosome Location	chr2:190015064-190015065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190010189..190015498-chr2:190084856..190090227,6	MCF-7	breast:
2	chr2:190012942..190018195-chr2:190085147..190088368,4	MCF-7	breast:
3	chr2:190014552..190015249-chr2:190149953..190150734,2	MCF-7	breast:
4	chr2:190009672..190012022-chr2:190013426..190016252,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10174225	0.81[ASN][1000 genomes]
rs10177513	0.81[ASN][1000 genomes]
rs10497699	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10931402	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10931406	0.91[ASN][1000 genomes]
rs10931410	0.91[ASN][1000 genomes]
rs11675295	0.91[ASN][1000 genomes]
rs11676812	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11678388	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11684869	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11691604	0.83[CEU][hapmap]
rs12472232	0.85[ASN][1000 genomes]
rs1515873	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1515875	0.82[ASN][1000 genomes]
rs17198773	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17198787	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17198829	0.91[ASN][1000 genomes]
rs17270952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17270966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17270973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17270987	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17271008	0.85[ASN][1000 genomes]
rs2680629	0.81[ASN][1000 genomes]
rs2683015	0.81[ASN][1000 genomes]
rs2683016	0.81[ASN][1000 genomes]
rs35598715	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55726777	0.92[ASN][1000 genomes]
rs55851872	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56252219	0.85[ASN][1000 genomes]
rs59031473	0.91[ASN][1000 genomes]
rs61130121	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62182067	0.81[ASN][1000 genomes]
rs62182415	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62182421	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182454	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182457	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62182458	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62182459	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62183794	0.91[ASN][1000 genomes]
rs62183841	0.91[ASN][1000 genomes]
rs62183844	0.91[ASN][1000 genomes]
rs62183845	0.91[ASN][1000 genomes]
rs72908368	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72908382	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72910347	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72910360	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7577872	0.81[ASN][1000 genomes]
rs7586853	0.85[ASN][1000 genomes]
rs9808245	0.81[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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189984000-190016800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:189993800-190017000	Weak transcription	Ovary	ovary
3	chr2:190009000-190016000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:190009800-190017200	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:190011200-190020800	Enhancers	NHDF-Ad	bronchial
6	chr2:190011600-190016200	Weak transcription	Fetal Lung	lung
7	chr2:190012200-190016800	Weak transcription	HSMMtube	muscle
8	chr2:190012400-190018000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:190012600-190017200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:190013200-190017000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:190013600-190017200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:190013800-190015200	Enhancers	Adipose Nuclei	Adipose
13	chr2:190014000-190016800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:190014200-190015600	Enhancers	Hela-S3	cervix
15	chr2:190014200-190016000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr2:190014200-190016800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:190014200-190017200	Enhancers	Osteobl	bone
18	chr2:190014400-190015200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:190014400-190015600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:190014400-190015600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr2:190014400-190016000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:190014600-190015200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:190014600-190015200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:190014600-190015200	Enhancers	Liver	Liver
25	chr2:190014600-190015400	Enhancers	Colon Smooth Muscle	Colon
26	chr2:190014600-190015600	Flanking Active TSS	A549	lung
27	chr2:190014600-190015800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:190014600-190019200	Enhancers	NHLF	lung
29	chr2:190014800-190015200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:190014800-190015200	Enhancers	Fetal Stomach	stomach
31	chr2:190014800-190015200	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr2:190014800-190015200	Genic enhancers	NH-A	brain
33	chr2:190014800-190015400	Enhancers	Aorta	Aorta
34	chr2:190014800-190016200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:190015000-190015400	Genic enhancers	HSMM	muscle
36	chr2:190015000-190016400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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