Variant report

Variant	rs1611371
Chromosome Location	chr6:29680021-29680022
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	POLR2A	chr6:29679868-29680305	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29675728..29678491-chr6:29678733..29681702,2	K562	blood:

Variant related genes	Relation type
ZDHHC20P1	TF binding region
ENSG00000233916	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1476572	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1476573	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610584	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610585	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610586	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610587	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610590	0.96[AFR][1000 genomes]
rs1610591	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1610592	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610593	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610594	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610595	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1610745	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1611356	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1611357	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1611358	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1611359	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1611360	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1611361	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1611362	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1611363	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611364	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1611365	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611366	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611368	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611369	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611370	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611372	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611375	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611376	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611377	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611378	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1611379	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1611380	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627465	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1736930	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1736931	0.99[AFR][1000 genomes]
rs2071653	0.80[ASN][1000 genomes]
rs2394659	0.91[AFR][1000 genomes]
rs2394660	0.94[AFR][1000 genomes]
rs2394661	0.82[AFR][1000 genomes]
rs2894114	0.94[AFR][1000 genomes]
rs3094726	0.94[AFR][1000 genomes]
rs3095285	0.93[ASN][1000 genomes]
rs3095291	0.82[ASN][1000 genomes]
rs3116788	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3116789	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3116790	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3116791	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3116792	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3116793	0.94[AFR][1000 genomes]
rs3116794	0.94[AFR][1000 genomes]
rs3116795	0.92[AFR][1000 genomes]
rs3116796	0.94[AFR][1000 genomes]
rs3116798	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3117290	0.82[ASN][1000 genomes]
rs3129029	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3129043	0.93[ASN][1000 genomes]
rs3129190	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3131854	0.80[ASN][1000 genomes]
rs3131863	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv10151	chr6:29679433-29682912	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1611371	ZKSCAN3	cis	cerebellum	SCAN
rs1611371	HLA-F	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29677400-29681200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:29677600-29681000	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr6:29677600-29681200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:29677600-29681400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:29677600-29682000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:29677600-29682600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:29677800-29681000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:29678200-29680600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:29678200-29681200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:29678400-29685200	Weak transcription	Esophagus	oesophagus
12	chr6:29678600-29681800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr6:29678600-29689200	Weak transcription	GM12878-XiMat	blood
14	chr6:29679200-29680600	Enhancers	Brain Hippocampus Middle	brain
15	chr6:29679200-29680800	Weak transcription	Spleen	Spleen
16	chr6:29679400-29680800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:29679600-29680400	Enhancers	Brain Cingulate Gyrus	brain
18	chr6:29679600-29683600	Weak transcription	Primary T cells from cord blood	blood
19	chr6:29680000-29681000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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