Variant report

Variant	rs9468141
Chromosome Location	chr6:27474527-27474528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27472071..27474860-chr6:27486354..27488722,3	K562	blood:
2	chr6:27471243..27473118-chr6:27473124..27475261,2	K562	blood:
3	chr6:27472621..27475271-chr6:27477554..27480516,2	MCF-7	breast:
4	chr6:27112845..27117785-chr6:27470908..27475349,7	K562	blood:
5	chr6:27474407..27478375-chr6:27478575..27482330,4	K562	blood:
6	chr6:27469947..27474974-chr6:27485508..27488698,9	K562	blood:

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 160 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs1014227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs1022486	0.82[YRI][hapmap]
rs1022515	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs10452601	0.96[ASN][1000 genomes]
rs10484398	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10755644	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs10807020	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs10807021	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs10807024	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10807025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10946913	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10946914	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10946919	0.90[ASN][1000 genomes]
rs10946920	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10946921	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10946931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10946932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[ASN][1000 genomes]
rs10946933	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.98[ASN][1000 genomes]
rs11968825	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11970336	0.92[ASN][1000 genomes]
rs12199110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12206045	0.96[ASN][1000 genomes]
rs12213598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs12215117	0.92[ASN][1000 genomes]
rs12524409	0.92[ASN][1000 genomes]
rs12529839	0.90[ASN][1000 genomes]
rs12662076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13201443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13201965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13201985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13212050	0.99[ASN][1000 genomes]
rs13215560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217162	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13217248	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13220155	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs1534937	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1883216	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1883404	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs1883405	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1985818	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2015648	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2049944	0.92[ASN][1000 genomes]
rs2049945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2064219	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2076305	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2092120	0.88[ASN][1000 genomes]
rs2092121	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2092122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2103557	0.86[ASN][1000 genomes]
rs2142705	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs2143062	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2179154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2205831	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2206250	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs2206251	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2206252	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2223463	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2223464	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2235252	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2235254	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2272814	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs2272815	0.90[ASN][1000 genomes]
rs2272816	0.91[ASN][1000 genomes]
rs2294308	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294309	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2393929	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2393931	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2893917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35394453	0.90[ASN][1000 genomes]
rs3734574	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs3734575	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4305708	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4358616	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs4455661	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4478400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4504471	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4711147	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4711148	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4711153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4713086	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4713092	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4713104	0.92[ASN][1000 genomes]
rs4713105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713106	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4713107	0.87[ASN][1000 genomes]
rs4713109	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62401365	0.92[ASN][1000 genomes]
rs6456774	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6456777	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6456778	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6456781	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6456785	0.83[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap]
rs6456786	0.90[ASN][1000 genomes]
rs6456788	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6456789	0.92[ASN][1000 genomes]
rs6650992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6899950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6903282	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6904844	0.96[ASN][1000 genomes]
rs6904883	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6911865	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915934	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6918131	0.98[ASN][1000 genomes]
rs6918794	0.83[ASN][1000 genomes]
rs6920010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6920362	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6920408	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs6920733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6921071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6923108	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6923539	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6929812	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6931659	0.94[ASN][1000 genomes]
rs6933354	0.98[ASN][1000 genomes]
rs6934748	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6934985	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6936356	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6936539	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6938943	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs726830	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7509	0.86[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs764460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs764461	0.92[ASN][1000 genomes]
rs766092	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs7741031	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[ASN][1000 genomes]
rs7743443	0.92[ASN][1000 genomes]
rs7743465	0.92[ASN][1000 genomes]
rs7744110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7745380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7748366	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7750795	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs7754411	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs7754678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs7754724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7754977	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs7756216	0.92[ASN][1000 genomes]
rs7756377	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7759001	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs7761989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7764070	0.92[ASN][1000 genomes]
rs7764634	0.87[ASN][1000 genomes]
rs7771590	0.99[ASN][1000 genomes]
rs7772160	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7774613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7776338	0.98[ASN][1000 genomes]
rs9357037	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs9461380	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9461386	0.86[ASN][1000 genomes]
rs9468101	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9468111	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9468115	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9468117	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9468140	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs980960	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs980961	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs980962	1.00[CHB][hapmap];0.95[JPT][hapmap]

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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9468141	ZSCAN23	cis	cerebellum	SCAN
rs9468141	ZNF391	cis	Artery Tibial	GTEx
rs9468141	ZNF391	cis	Heart Left Ventricle	GTEx
rs9468141	DCDC2	cis	cerebellum	SCAN
rs9468141	ZNF391	cis	lymphoblastoid	seeQTL
rs9468141	ZNF391	cis	cerebellum	SCAN
rs9468141	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs9468141	ZNF391	cis	Esophagus Muscularis	GTEx
rs9468141	ZNF204P	cis	parietal	SCAN
rs9468141	ZNF391	cis	lung	GTEx
rs9468141	ZNF391	cis	parietal	SCAN
rs9468141	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27471600-27479800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:27471800-27474600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:27473200-27475200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27473800-27475400	Enhancers	Hela-S3	cervix
5	chr6:27474200-27474600	Flanking Active TSS	A549	lung
6	chr6:27474200-27474600	Enhancers	HepG2	liver
7	chr6:27474200-27474800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:27474200-27474800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:27474200-27480000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:27474400-27474600	Enhancers	K562	blood

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