Variant report

Variant	rs60693965
Chromosome Location	chr1:227512190-227512191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227510419..227513030-chr1:227581221..227583302,2	K562	blood:
2	chr1:227510624..227512509-chr1:227521394..227523406,2	K562	blood:
3	chr1:227511186..227513689-chr1:227514220..227516640,3	K562	blood:
4	chr1:227511205..227513066-chr1:227516243..227518388,2	MCF-7	breast:
5	chr1:227510287..227513038-chr1:227518818..227521633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234277	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10495251	0.85[ASN][1000 genomes]
rs10495252	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10495254	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916115	0.85[ASN][1000 genomes]
rs11799960	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11800390	0.85[ASN][1000 genomes]
rs11800982	0.83[ASN][1000 genomes]
rs11801500	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11801885	0.84[ASN][1000 genomes]
rs11802394	0.84[ASN][1000 genomes]
rs11804613	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11804709	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11805097	0.85[ASN][1000 genomes]
rs11805221	0.84[ASN][1000 genomes]
rs11805679	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11805859	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11806180	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11806188	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11807620	0.96[ASN][1000 genomes]
rs11810471	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11811972	0.84[ASN][1000 genomes]
rs11812018	0.80[EUR][1000 genomes]
rs12407020	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12407033	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12409411	0.82[ASN][1000 genomes]
rs12410073	0.84[ASN][1000 genomes]
rs12410267	0.82[ASN][1000 genomes]
rs1464075	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1513621	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16847571	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16847574	0.83[ASN][1000 genomes]
rs16847582	0.85[ASN][1000 genomes]
rs16847612	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16847617	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16847618	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16847625	0.96[ASN][1000 genomes]
rs16847628	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16847631	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16847643	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16847647	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16847649	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2670443	0.85[AMR][1000 genomes]
rs2670448	0.85[AMR][1000 genomes]
rs2670466	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2670472	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2718198	0.84[AMR][1000 genomes]
rs2718199	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2718213	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2718218	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2813946	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2813951	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2813952	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2813954	0.83[AMR][1000 genomes]
rs2813981	0.85[AMR][1000 genomes]
rs3127003	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3795456	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4233223	0.84[ASN][1000 genomes]
rs4276876	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4281297	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4284230	0.95[ASN][1000 genomes]
rs4292922	0.95[ASN][1000 genomes]
rs4298700	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4306096	0.84[ASN][1000 genomes]
rs4344297	0.93[ASN][1000 genomes]
rs4415529	0.94[ASN][1000 genomes]
rs4500280	0.94[ASN][1000 genomes]
rs4545305	0.82[ASN][1000 genomes]
rs4568795	0.93[ASN][1000 genomes]
rs4653488	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653490	0.95[ASN][1000 genomes]
rs4653492	0.93[ASN][1000 genomes]
rs4653493	0.91[ASN][1000 genomes]
rs4653494	0.91[ASN][1000 genomes]
rs4653814	0.81[ASN][1000 genomes]
rs4653816	0.94[ASN][1000 genomes]
rs4653817	0.94[ASN][1000 genomes]
rs4653818	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4653819	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4653820	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4653821	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs56703671	0.82[ASN][1000 genomes]
rs56830706	0.85[ASN][1000 genomes]
rs58442442	0.85[ASN][1000 genomes]
rs58912604	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59187211	0.95[ASN][1000 genomes]
rs59472079	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59562576	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59596249	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs59981133	0.85[ASN][1000 genomes]
rs60115015	0.85[ASN][1000 genomes]
rs60117206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60585433	0.85[ASN][1000 genomes]
rs60592061	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs66475802	0.85[ASN][1000 genomes]
rs66523880	0.95[ASN][1000 genomes]
rs66738032	0.96[ASN][1000 genomes]
rs66765246	0.95[ASN][1000 genomes]
rs6691882	0.95[ASN][1000 genomes]
rs6693234	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6700070	0.81[AMR][1000 genomes]
rs67070254	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67316436	0.85[ASN][1000 genomes]
rs67343460	0.84[ASN][1000 genomes]
rs67400293	0.85[ASN][1000 genomes]
rs67715027	0.85[ASN][1000 genomes]
rs67723257	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs68043093	0.96[ASN][1000 genomes]
rs68077109	0.95[ASN][1000 genomes]
rs68133756	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72632805	0.80[ASN][1000 genomes]
rs72632806	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72632807	0.83[ASN][1000 genomes]
rs72632809	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72632810	0.84[ASN][1000 genomes]
rs72632811	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72632812	0.84[ASN][1000 genomes]
rs72632813	0.84[ASN][1000 genomes]
rs72632814	0.84[ASN][1000 genomes]
rs72632815	0.85[ASN][1000 genomes]
rs72632816	0.85[ASN][1000 genomes]
rs72632818	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72632819	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs72632820	0.94[ASN][1000 genomes]
rs72632821	0.96[ASN][1000 genomes]
rs72632822	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72632823	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72632824	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72632825	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513776	0.96[ASN][1000 genomes]
rs7514796	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7519849	0.85[ASN][1000 genomes]
rs7520769	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7530080	0.85[ASN][1000 genomes]
rs7540775	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541220	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7541499	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7549515	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549619	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7552957	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7554168	0.96[ASN][1000 genomes]
rs7556319	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9426548	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9426619	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60693965	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227507000-227515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:227507200-227518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:227508400-227512200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:227509400-227516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:227510400-227516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:227510800-227512200	Flanking Active TSS	Hela-S3	cervix
7	chr1:227511600-227512200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:227511600-227515600	Weak transcription	Liver	Liver
9	chr1:227511600-227518000	Weak transcription	K562	blood
10	chr1:227512000-227516400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:227512000-227523200	Weak transcription	Stomach Mucosa	stomach

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