Variant report

Variant	rs1165200
Chromosome Location	chr6:25875212-25875213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1165188	0.83[YRI][hapmap]
rs12192635	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs12200962	0.83[CEU][hapmap];0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs12201170	0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs17270561	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap]
rs17271767	0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs579996	0.84[YRI][hapmap]
rs603089	0.92[GIH][hapmap]
rs717551	0.83[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.80[TSI][hapmap];0.85[EUR][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
5	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
6	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1165200	SLC17A4	cis	parietal	SCAN
rs1165200	HIST1H4I	cis	cerebellum	SCAN
rs1165200	ZNF391	cis	cerebellum	SCAN
rs1165200	HIST1H1C	cis	parietal	SCAN
rs1165200	HIST1H2BF	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25872800-25875800	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr6:25873000-25876400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:25873000-25877000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:25873000-25877000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:25873800-25876400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:25874200-25875800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:25874200-25877400	Enhancers	HepG2	liver
8	chr6:25874400-25875400	Active TSS	A549	lung
9	chr6:25874600-25875400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:25874800-25875800	Enhancers	Primary T cells from cord blood	blood
11	chr6:25874800-25877200	Enhancers	Liver	Liver
12	chr6:25875000-25875400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr6:25875000-25875600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr6:25875000-25875800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr6:25875000-25875800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:25875200-25875400	Bivalent Enhancer	Dnd41	blood
17	chr6:25875200-25875600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:25875200-25875600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:25875200-25875800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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