Variant report

Variant	rs7743187
Chromosome Location	chr6:25028663-25028664
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	CTCF	chr6:25028620-25028770	GM12864	blood:	n/a	n/a
2	CTCF	chr6:25028540-25028690	GM12872	blood:	n/a	n/a
3	CTCF	chr6:25028579-25028714	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25028396..25029900-chr6:25034648..25037120,2	K562	blood:
2	chr6:25027553..25029661-chr6:25041949..25043586,2	MCF-7	breast:

Variant related genes	Relation type
ASS1P1	TF binding region
ENSG00000229313	Chromatin interaction
ENSG00000272053	Chromatin interaction
ENSG00000111913	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1410688	0.87[GIH][hapmap]
rs6456645	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930521	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724651	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7767457	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7743187	LRRC16A	cis	parietal	SCAN
rs7743187	C6orf62	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25011200-25035600	Weak transcription	Spleen	Spleen
2	chr6:25026400-25033600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:25027800-25028800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:25027800-25029200	Enhancers	Primary hematopoietic stem cells	blood
5	chr6:25028000-25030600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:25028200-25030600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:25028200-25032200	Weak transcription	Thymus	Thymus
8	chr6:25028200-25032400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:25028200-25033600	Weak transcription	Primary B cells from cord blood	blood
10	chr6:25028200-25033600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:25028200-25034600	Weak transcription	Primary T cells from cord blood	blood
12	chr6:25028200-25035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:25028200-25037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:25028400-25028800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr6:25028400-25029000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:25028400-25029200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:25028400-25029200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:25028400-25033600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:25028400-25033600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:25028400-25033600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:25028600-25028800	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr6:25028600-25028800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:25028600-25028800	Enhancers	Fetal Brain Female	brain
24	chr6:25028600-25029000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:25028600-25032400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:25028600-25032800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:25028600-25033000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:25028600-25033200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:25028600-25033600	Weak transcription	Dnd41	blood
30	chr6:25028600-25034400	Weak transcription	Fetal Thymus	thymus
31	chr6:25028600-25034600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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