Variant report

Variant	rs3011302
Chromosome Location	chr6:81208139-81208140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs11961045	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1370137	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1436867	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1436868	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436871	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1698337	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1816564	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs1821786	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1836961	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1865917	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164606	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164607	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164608	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164610	0.86[EUR][1000 genomes]
rs2322770	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2437879	0.88[EUR][1000 genomes]
rs2917605	0.86[EUR][1000 genomes]
rs2917606	0.89[EUR][1000 genomes]
rs2917607	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2917608	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011299	0.91[EUR][1000 genomes]
rs3011300	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011301	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011304	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4635986	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4637601	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs484264	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484560	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs485088	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486271	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487328	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs488098	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505678	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs506825	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs508759	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs512946	0.95[EUR][1000 genomes]
rs514517	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515347	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520099	0.89[EUR][1000 genomes]
rs520139	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522183	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs528886	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs529744	0.89[EUR][1000 genomes]
rs532709	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535350	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs536598	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs538905	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540896	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs541446	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548876	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553433	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs558478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs559034	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs560068	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs560909	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56112536	0.89[ASN][1000 genomes]
rs564757	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs567324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs568155	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs568253	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572007	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs574098	0.94[ASN][1000 genomes]
rs577129	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs577892	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs580525	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs581715	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs582966	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584904	0.89[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs585229	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586593	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586605	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588876	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593167	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs594567	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs595791	0.91[EUR][1000 genomes]
rs596723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs597937	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs597950	0.88[EUR][1000 genomes]
rs598382	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600549	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610292	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs612684	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613998	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614483	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615815	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622089	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622117	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622849	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs623286	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs623367	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs624645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625136	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs630687	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs631481	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs632397	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs634504	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs642613	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs645216	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454158	0.86[ASN][1000 genomes]
rs654625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654955	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs655350	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs656381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661076	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661119	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66969849	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67220910	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs674031	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675769	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs681085	0.86[EUR][1000 genomes]
rs687203	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs694288	0.89[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs694756	0.89[EUR][1000 genomes]
rs73473458	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7752733	0.93[AMR][1000 genomes]
rs7752861	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7753440	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7757432	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772873	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs893126	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9294175	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9343998	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9352834	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9352838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9361616	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9361617	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9443781	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9449007	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1019670	chr6:81086504-81569984	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv915714	chr6:81134888-81366749	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1019932	chr6:81155458-81217868	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv886311	chr6:81166178-81239971	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv886312	chr6:81166178-81309481	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv886313	chr6:81177227-81239971	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3011302	PHIP	cis	parietal	SCAN
rs3011302	LCA5	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81207400-81208200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:81207600-81208200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:81207600-81208200	Active TSS	Fetal Intestine Small	intestine
4	chr6:81207600-81208200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr6:81207600-81208200	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr6:81207600-81208400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:81207600-81208400	Active TSS	Duodenum Mucosa	Duodenum
8	chr6:81207800-81208200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr6:81207800-81208400	Enhancers	Fetal Intestine Large	intestine
10	chr6:81208000-81208200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:81208000-81208600	Enhancers	HepG2	liver
12	chr6:81208000-81208800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:81208000-81222600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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