Variant report

Variant	rs3862151
Chromosome Location	chr17:19957289-19957290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr17:19956990-19957306	K562	blood:	n/a	n/a
2	KAP1	chr17:19956644-19957363	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19950835..19953752-chr17:19957285..19959162,2	K562	blood:
2	chr17:19957156..19957918-chr17:21191377..21192085,2	Hela-S3	cervix:
3	chr17:19957236..19958763-chr17:19963646..19966262,2	K562	blood:
4	chr17:19911303..19913240-chr17:19956508..19959161,2	K562	blood:

Variant related genes	Relation type
ENSG00000225681	TF binding region
ENSG00000261033	Chromatin interaction
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10083830	1.00[ASN][1000 genomes]
rs10083840	1.00[ASN][1000 genomes]
rs1009082	1.00[CHB][hapmap]
rs10438824	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs11869931	0.93[AMR][1000 genomes]
rs12449914	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450857	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12453332	0.91[AMR][1000 genomes]
rs12453720	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs12936794	0.92[AFR][1000 genomes]
rs12937327	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943904	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12944084	0.92[AFR][1000 genomes]
rs12946508	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12947713	0.93[AMR][1000 genomes]
rs12947950	1.00[CHB][hapmap]
rs12948178	0.81[EUR][1000 genomes]
rs12949485	1.00[CHB][hapmap]
rs12949710	0.93[AMR][1000 genomes]
rs1468953	0.93[AMR][1000 genomes]
rs1544421	1.00[CHB][hapmap]
rs1638527	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17604987	1.00[CHB][hapmap]
rs17685923	0.93[AMR][1000 genomes]
rs17686622	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs17686839	1.00[CHB][hapmap]
rs17759041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17759083	1.00[ASN][1000 genomes]
rs17759609	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1812934	1.00[CHB][hapmap]
rs203467	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs203475	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs203480	1.00[CHB][hapmap]
rs2107566	1.00[CHB][hapmap]
rs2108981	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2158473	1.00[CHB][hapmap]
rs2189710	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2263175	1.00[CHB][hapmap]
rs2386485	1.00[CHB][hapmap]
rs2526460	1.00[CHB][hapmap]
rs2526462	1.00[CHB][hapmap]
rs2526471	1.00[CHB][hapmap]
rs2526474	1.00[CHB][hapmap]
rs2526475	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2526480	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2526484	1.00[CHB][hapmap]
rs2526491	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap]
rs2703772	1.00[CHB][hapmap]
rs2703773	1.00[CHB][hapmap]
rs2703774	1.00[CHB][hapmap]
rs2703782	1.00[CHB][hapmap]
rs2703794	1.00[CHB][hapmap]
rs2703799	1.00[CHB][hapmap]
rs2703801	1.00[CHB][hapmap]
rs2703802	1.00[CHB][hapmap]
rs2703804	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2703806	1.00[CHB][hapmap]
rs2703808	1.00[CHB][hapmap]
rs2703813	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs2703815	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2703816	1.00[CHB][hapmap]
rs2703817	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2703818	1.00[CHB][hapmap]
rs2703821	1.00[CHB][hapmap]
rs34089239	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs34756775	0.93[AMR][1000 genomes]
rs35124809	0.93[AMR][1000 genomes]
rs35156798	0.93[AMR][1000 genomes]
rs35191778	0.93[AMR][1000 genomes]
rs35244101	0.93[AMR][1000 genomes]
rs35254155	0.92[AFR][1000 genomes]
rs35315252	0.88[AFR][1000 genomes]
rs35317166	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35493088	0.93[AMR][1000 genomes]
rs35770292	0.93[AMR][1000 genomes]
rs35915823	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341795	0.93[AMR][1000 genomes]
rs4346259	0.93[AMR][1000 genomes]
rs4350625	0.93[AMR][1000 genomes]
rs4471741	0.91[AMR][1000 genomes]
rs4577147	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4588033	1.00[CHB][hapmap]
rs4924802	1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924809	1.00[CHB][hapmap]
rs4924810	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4925054	1.00[CHB][hapmap]
rs4925071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925075	0.91[GIH][hapmap];0.87[MEX][hapmap];0.93[AMR][1000 genomes]
rs4925076	0.93[AMR][1000 genomes]
rs4925078	0.93[AMR][1000 genomes]
rs4925084	1.00[CHB][hapmap];0.90[AMR][1000 genomes]
rs56371654	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62067482	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62067483	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62067488	0.93[AMR][1000 genomes]
rs7503407	0.93[AMR][1000 genomes]
rs8068484	0.91[AMR][1000 genomes]
rs8075343	0.93[AMR][1000 genomes]
rs8081817	0.93[AMR][1000 genomes]
rs850622	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1066594	chr17:19947874-19986671	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv543259	chr17:19947874-19986671	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3862151	CYTSB	cis	cerebellum	SCAN
rs3862151	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs3862151	AKAP10	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19943800-19965800	Weak transcription	Aorta	Aorta
2	chr17:19948200-19966400	Weak transcription	Brain Angular Gyrus	brain
3	chr17:19950800-19966400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:19956600-19957400	ZNF genes & repeats	A549	lung
5	chr17:19956800-19957400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:19956800-19957400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr17:19957000-19962600	Weak transcription	K562	blood
8	chr17:19957000-19965800	Weak transcription	Ovary	ovary
9	chr17:19957000-19967000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:19957200-19962600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr17:19957200-19962800	Weak transcription	Brain Hippocampus Middle	brain

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