Variant report

Variant	rs1861509
Chromosome Location	chr2:206177750-206177751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:206176311..206178033-chr2:206179615..206181550,2	MCF-7	breast:

Extended variants
information (count: 177 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:174)

rs_ID	r²[population]
rs10199654	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10205892	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10490290	0.88[ASN][1000 genomes]
rs10490292	0.88[ASN][1000 genomes]
rs10490293	0.88[ASN][1000 genomes]
rs10490295	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10804147	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10804148	0.83[ASN][1000 genomes]
rs10932102	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932104	0.91[ASN][1000 genomes]
rs10932105	0.90[ASN][1000 genomes]
rs10932106	0.90[ASN][1000 genomes]
rs10932107	0.88[ASN][1000 genomes]
rs10932108	0.88[ASN][1000 genomes]
rs10932109	0.87[ASN][1000 genomes]
rs1113314	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11676344	0.86[ASN][1000 genomes]
rs11676518	0.88[ASN][1000 genomes]
rs11676519	0.88[ASN][1000 genomes]
rs11676529	0.88[ASN][1000 genomes]
rs11677457	0.92[ASN][1000 genomes]
rs11686270	0.88[ASN][1000 genomes]
rs11690439	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11690480	0.92[ASN][1000 genomes]
rs11690561	0.92[ASN][1000 genomes]
rs11691342	0.89[ASN][1000 genomes]
rs11691345	0.90[ASN][1000 genomes]
rs11692923	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695465	0.92[ASN][1000 genomes]
rs1207411	0.89[ASN][1000 genomes]
rs1207415	0.90[ASN][1000 genomes]
rs1207426	0.81[ASN][1000 genomes]
rs1207430	0.81[ASN][1000 genomes]
rs1207431	0.81[ASN][1000 genomes]
rs1207432	0.81[ASN][1000 genomes]
rs1207433	0.81[ASN][1000 genomes]
rs1207434	0.82[ASN][1000 genomes]
rs1207435	0.84[ASN][1000 genomes]
rs1207436	0.84[ASN][1000 genomes]
rs1207437	0.84[ASN][1000 genomes]
rs1207438	0.84[ASN][1000 genomes]
rs1207440	0.90[ASN][1000 genomes]
rs1207441	0.90[ASN][1000 genomes]
rs1211319	0.80[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12373584	0.88[ASN][1000 genomes]
rs12373610	0.88[ASN][1000 genomes]
rs12464688	0.88[ASN][1000 genomes]
rs12464755	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468755	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12468794	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12468975	0.89[ASN][1000 genomes]
rs12470003	0.88[ASN][1000 genomes]
rs12470079	0.88[ASN][1000 genomes]
rs12470434	0.93[ASN][1000 genomes]
rs12472752	0.86[ASN][1000 genomes]
rs12472815	0.85[ASN][1000 genomes]
rs12474300	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12476682	0.92[ASN][1000 genomes]
rs12615597	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622101	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623757	0.92[ASN][1000 genomes]
rs12989507	0.92[ASN][1000 genomes]
rs12995657	0.87[ASN][1000 genomes]
rs13000324	0.88[ASN][1000 genomes]
rs13002238	0.91[ASN][1000 genomes]
rs13004164	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13004568	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13009974	0.92[ASN][1000 genomes]
rs13011880	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13011981	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13015412	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13017922	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13021602	0.87[ASN][1000 genomes]
rs13022810	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13024741	0.83[ASN][1000 genomes]
rs13024952	0.84[ASN][1000 genomes]
rs13025642	0.81[ASN][1000 genomes]
rs13028215	0.85[ASN][1000 genomes]
rs13033820	0.85[ASN][1000 genomes]
rs1398053	0.88[ASN][1000 genomes]
rs1398054	0.88[ASN][1000 genomes]
rs1511873	0.92[ASN][1000 genomes]
rs1511874	0.92[ASN][1000 genomes]
rs1540365	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1540366	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1540367	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1540368	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1540369	0.92[ASN][1000 genomes]
rs1606238	0.92[ASN][1000 genomes]
rs1606239	0.92[ASN][1000 genomes]
rs17201041	0.92[ASN][1000 genomes]
rs1849226	0.82[ASN][1000 genomes]
rs1861508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861514	0.92[ASN][1000 genomes]
rs1877338	0.88[ASN][1000 genomes]
rs1877339	0.88[ASN][1000 genomes]
rs1912845	0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1921805	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041877	0.90[ASN][1000 genomes]
rs2080418	0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs2080419	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2160455	0.93[ASN][1000 genomes]
rs2193077	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2251539	0.81[ASN][1000 genomes]
rs2336416	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336417	0.92[ASN][1000 genomes]
rs2336418	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2336419	0.94[EUR][1000 genomes]
rs2336420	0.88[ASN][1000 genomes]
rs2541151	0.84[ASN][1000 genomes]
rs2541152	0.84[ASN][1000 genomes]
rs2541153	0.84[ASN][1000 genomes]
rs2541154	0.84[ASN][1000 genomes]
rs2704643	0.90[ASN][1000 genomes]
rs2704644	0.84[ASN][1000 genomes]
rs2878692	0.81[ASN][1000 genomes]
rs34226321	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34332011	0.87[ASN][1000 genomes]
rs34486316	0.88[ASN][1000 genomes]
rs35337631	0.88[ASN][1000 genomes]
rs35550118	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3843339	0.93[ASN][1000 genomes]
rs3845806	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3856509	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3928642	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4119079	1.00[ASN][1000 genomes]
rs4119081	1.00[ASN][1000 genomes]
rs4505506	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs4595957	0.87[ASN][1000 genomes]
rs4673318	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4673319	0.93[ASN][1000 genomes]
rs4673320	0.92[ASN][1000 genomes]
rs4673323	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4673324	0.90[ASN][1000 genomes]
rs4673325	0.86[ASN][1000 genomes]
rs4673326	0.88[ASN][1000 genomes]
rs4673327	0.88[ASN][1000 genomes]
rs4673328	0.88[ASN][1000 genomes]
rs4673329	0.87[ASN][1000 genomes]
rs4673330	0.87[ASN][1000 genomes]
rs4675508	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4675510	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4675511	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675512	0.86[ASN][1000 genomes]
rs4675513	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675515	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4675519	0.92[ASN][1000 genomes]
rs4675521	0.85[ASN][1000 genomes]
rs55850246	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62171496	0.84[ASN][1000 genomes]
rs62171506	0.92[ASN][1000 genomes]
rs66583439	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6740963	0.88[ASN][1000 genomes]
rs6755865	0.87[ASN][1000 genomes]
rs6756234	0.84[ASN][1000 genomes]
rs6758445	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6761373	0.93[ASN][1000 genomes]
rs7582340	0.88[ASN][1000 genomes]
rs7594732	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs849189	0.84[ASN][1000 genomes]
rs849193	0.82[ASN][1000 genomes]
rs849194	0.84[ASN][1000 genomes]
rs849216	0.82[ASN][1000 genomes]
rs849218	0.84[ASN][1000 genomes]
rs849219	0.84[ASN][1000 genomes]
rs849220	0.83[ASN][1000 genomes]
rs849221	0.84[ASN][1000 genomes]
rs849222	0.84[ASN][1000 genomes]
rs849223	0.84[ASN][1000 genomes]
rs849250	0.81[ASN][1000 genomes]
rs907462	0.89[EUR][1000 genomes]
rs964896	0.88[ASN][1000 genomes]
rs964897	0.88[ASN][1000 genomes]
rs979187	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998485	chr2:205407813-206184006	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536122	chr2:205407813-206184006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1012780	chr2:206124954-206546271	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1861509	PARD3B	cis	cerebellum	SCAN
rs1861509	ALS2CR12	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:206168600-206190600	Weak transcription	Fetal Intestine Large	intestine
2	chr2:206171000-206183400	Weak transcription	Aorta	Aorta
3	chr2:206171000-206186200	Weak transcription	HSMMtube	muscle
4	chr2:206171000-206190200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:206172600-206185400	Weak transcription	HSMM	muscle
6	chr2:206176200-206177800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:206177000-206177800	Enhancers	Colon Smooth Muscle	Colon
8	chr2:206177200-206178200	Enhancers	Fetal Lung	lung

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