Variant report

Variant	rs1986602
Chromosome Location	chr12:86725132-86725133
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	chr12:86723150..86725256-chr12:86785265..86787177,2	MCF-7	breast:

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10745407	0.84[JPT][hapmap]
rs10745408	0.83[JPT][hapmap]
rs10776955	0.83[JPT][hapmap]
rs10858408	0.84[JPT][hapmap]
rs10858415	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs11103930	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs11830208	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs11830448	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11835193	1.00[EUR][1000 genomes]
rs12302310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12303046	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes]
rs12319410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12319593	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579580	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12581639	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12581912	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582767	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1493415	0.81[JPT][hapmap]
rs1628799	1.00[JPT][hapmap]
rs1698787	0.84[JPT][hapmap]
rs17013792	0.82[YRI][hapmap]
rs17013858	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17013981	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17014005	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17014008	1.00[JPT][hapmap]
rs17014009	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17014020	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs17014026	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17040806	0.87[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap]
rs1986603	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1994863	1.00[JPT][hapmap]
rs2141927	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2220782	0.83[JPT][hapmap]
rs2405793	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2405929	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405931	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs2406116	0.83[JPT][hapmap]
rs2406118	0.83[JPT][hapmap]
rs2406122	0.83[JPT][hapmap]
rs2406123	0.84[JPT][hapmap]
rs2406127	0.84[JPT][hapmap]
rs2406128	0.83[JPT][hapmap]
rs2406160	0.84[JPT][hapmap]
rs2452807	0.84[JPT][hapmap]
rs2465144	0.84[JPT][hapmap]
rs2471560	0.83[JPT][hapmap]
rs2471568	0.84[JPT][hapmap]
rs2471569	0.84[JPT][hapmap]
rs2897240	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2897274	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897275	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes]
rs2897277	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2897278	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4370997	0.84[JPT][hapmap]
rs4488269	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs4526834	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs4636736	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56170210	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57002922	0.85[AMR][1000 genomes]
rs57977247	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58054764	1.00[EUR][1000 genomes]
rs59690693	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60555693	0.85[AMR][1000 genomes]
rs60902071	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61014498	0.85[AMR][1000 genomes]
rs61359740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61571841	1.00[EUR][1000 genomes]
rs61950714	0.91[ASN][1000 genomes]
rs6538023	1.00[JPT][hapmap]
rs6538024	1.00[JPT][hapmap]
rs6538025	0.83[JPT][hapmap]
rs6538029	0.84[JPT][hapmap]
rs7135177	0.83[JPT][hapmap]
rs7138352	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7138786	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7301129	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs73385292	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73385293	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73387865	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953196	0.83[JPT][hapmap]
rs7953491	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7961251	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs7964553	0.84[JPT][hapmap]
rs7973773	0.84[JPT][hapmap]
rs7977034	0.81[YRI][hapmap]
rs7980126	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs839104	0.83[JPT][hapmap]
rs839148	0.83[JPT][hapmap]
rs839149	0.84[JPT][hapmap]
rs839150	0.80[JPT][hapmap]
rs839151	0.84[JPT][hapmap]
rs839152	0.86[JPT][hapmap]
rs839153	0.84[JPT][hapmap]
rs839156	0.84[JPT][hapmap]
rs839157	0.83[JPT][hapmap]
rs839158	0.83[JPT][hapmap]
rs839159	0.84[JPT][hapmap]
rs839162	1.00[JPT][hapmap]
rs839165	0.83[JPT][hapmap]
rs839166	0.84[JPT][hapmap]
rs839168	0.84[JPT][hapmap]
rs839170	0.83[JPT][hapmap]
rs839171	0.83[JPT][hapmap]
rs844434	0.83[JPT][hapmap]
rs844435	0.83[JPT][hapmap]
rs863392	0.83[JPT][hapmap]
rs863395	0.83[JPT][hapmap]
rs865138	0.84[JPT][hapmap]
rs865721	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1845250	chr12:86696771-86730126	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1053234	chr12:86701070-86774957	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	esv2754127	chr12:86723232-87576932	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86723800-86725400	Enhancers	Fetal Kidney	kidney
2	chr12:86723800-86726000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr12:86724600-86725200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:86724600-86726000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:86724600-86726400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr12:86724800-86725200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:86724800-86725400	Enhancers	Small Intestine	intestine
8	chr12:86724800-86725600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr12:86724800-86725600	Enhancers	Fetal Muscle Leg	muscle
10	chr12:86724800-86725800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:86724800-86725800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr12:86724800-86726400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr12:86724800-86727600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:86725000-86725200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:86725000-86725200	Enhancers	Fetal Brain Male	brain
16	chr12:86725000-86725400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr12:86725000-86725400	Enhancers	Adipose Nuclei	Adipose
18	chr12:86725000-86725400	Enhancers	Brain Germinal Matrix	brain
19	chr12:86725000-86725400	Enhancers	Fetal Lung	lung
20	chr12:86725000-86725600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:86725000-86725600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:86725000-86726000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr12:86725000-86726000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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