Variant report

Variant	rs1354902
Chromosome Location	chr2:189460696-189460697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:189460620..189463074-chr2:189843714..189846986,3	MCF-7	breast:
2	chr2:189449607..189454566-chr2:189458525..189463315,5	MCF-7	breast:
3	chr13:92777089..92778054-chr2:189460184..189460902,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144366	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10173369	0.83[EUR][1000 genomes]
rs10199260	1.00[JPT][hapmap]
rs10211141	0.82[ASN][1000 genomes]
rs1066766	0.89[EUR][1000 genomes]
rs10804021	1.00[JPT][hapmap]
rs10931363	1.00[JPT][hapmap]
rs10931369	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11683089	0.81[EUR][1000 genomes]
rs11683183	0.81[EUR][1000 genomes]
rs11686702	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11695316	1.00[JPT][hapmap]
rs12463744	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12475894	1.00[JPT][hapmap]
rs12476413	1.00[JPT][hapmap]
rs12693504	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13012993	0.85[AMR][1000 genomes]
rs13025659	1.00[JPT][hapmap]
rs13386959	1.00[JPT][hapmap]
rs13392850	1.00[JPT][hapmap]
rs13393057	1.00[JPT][hapmap]
rs13396968	1.00[JPT][hapmap]
rs13397653	1.00[JPT][hapmap]
rs13412448	1.00[JPT][hapmap]
rs13414327	1.00[JPT][hapmap]
rs13418031	1.00[JPT][hapmap]
rs1354904	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1354908	0.80[EUR][1000 genomes]
rs1354910	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1395869	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1507551	1.00[JPT][hapmap]
rs1507560	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1507561	0.80[EUR][1000 genomes]
rs1567184	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1580993	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1588121	0.89[EUR][1000 genomes]
rs1605460	0.84[EUR][1000 genomes]
rs16830169	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2882532	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3935690	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4146571	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4423571	0.92[ASN][1000 genomes]
rs4453658	1.00[JPT][hapmap]
rs4591284	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4667229	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4667231	1.00[JPT][hapmap]
rs58633000	0.92[ASN][1000 genomes]
rs6434291	0.84[EUR][1000 genomes]
rs6434292	0.84[EUR][1000 genomes]
rs6707212	1.00[JPT][hapmap]
rs6708451	0.81[EUR][1000 genomes]
rs6709557	1.00[JPT][hapmap]
rs6744275	1.00[JPT][hapmap]
rs6756504	1.00[JPT][hapmap]
rs698552	0.89[EUR][1000 genomes]
rs698554	0.89[EUR][1000 genomes]
rs698556	0.89[EUR][1000 genomes]
rs698557	0.87[EUR][1000 genomes]
rs7419798	1.00[JPT][hapmap]
rs7420808	1.00[JPT][hapmap]
rs7422739	1.00[JPT][hapmap]
rs7423554	1.00[JPT][hapmap]
rs7425417	0.90[CEU][hapmap]
rs7569960	0.92[ASN][1000 genomes]
rs7573579	0.92[ASN][1000 genomes]
rs7577912	0.84[EUR][1000 genomes]
rs7582643	1.00[JPT][hapmap]
rs7587596	1.00[JPT][hapmap]
rs7596299	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7599978	0.83[EUR][1000 genomes]
rs7602180	1.00[JPT][hapmap]
rs781283	0.81[CEU][hapmap]
rs781284	0.81[CEU][hapmap]
rs781286	0.81[CEU][hapmap]
rs781288	0.81[CEU][hapmap]
rs8273	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv834489	chr2:189329027-189494224	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv533110	chr2:189354436-189462552	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189420600-189463200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:189431400-189463200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:189434400-189463200	Weak transcription	Fetal Intestine Large	intestine
4	chr2:189434400-189465000	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:189436400-189463200	Weak transcription	Ovary	ovary
6	chr2:189443800-189464000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:189445800-189463400	Weak transcription	NHLF	lung
8	chr2:189446200-189461000	Weak transcription	Adipose Nuclei	Adipose
9	chr2:189450200-189463800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:189450400-189462000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:189450400-189463200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:189450400-189470600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:189450400-189475000	Weak transcription	Aorta	Aorta
14	chr2:189450600-189461400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:189450600-189463400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:189450600-189463400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:189450600-189463800	Weak transcription	Fetal Lung	lung
18	chr2:189450600-189464000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:189450600-189464000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:189450800-189460800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:189452800-189463200	Weak transcription	A549	lung
22	chr2:189453600-189463000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:189453600-189463400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:189455000-189461000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:189455200-189461800	Weak transcription	HUVEC	blood vessel
26	chr2:189455600-189463400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:189458600-189461800	Strong transcription	Placenta	Placenta
28	chr2:189459000-189465400	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr2:189459800-189463000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:189460000-189460800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:189460000-189465400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:189460400-189461200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:189460400-189461200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:189460400-189461400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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