Variant report

Variant	rs2394360
Chromosome Location	chr6:25031372-25031373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25024268..25027647-chr6:25028842..25032564,4	K562	blood:
2	chr6:25029897..25032330-chr6:25040931..25043429,2	K562	blood:
3	chr6:25023746..25026604-chr6:25028842..25032564,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMAHP-3	chr6:25031243-25031510	NONHSAT108130

Variant related genes	Relation type
ENSG00000220517	Chromatin interaction
ENSG00000272053	Chromatin interaction
ENSG00000229313	Chromatin interaction
ENSG00000111913	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10806997	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946741	0.82[EUR][1000 genomes]
rs10946742	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712879	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4712880	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918101	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv3421319	chr6:25030798-25033346	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
8	esv3392139	chr6:25031173-25033071	Genic enhancers Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2394360	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr6:25028200-25032200	Weak transcription	Thymus	Thymus
4	chr6:25028200-25032400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:25028200-25033600	Weak transcription	Primary B cells from cord blood	blood
6	chr6:25028200-25033600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:25028200-25034600	Weak transcription	Primary T cells from cord blood	blood
8	chr6:25028200-25035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:25028200-25037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:25028400-25033600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:25028400-25033600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:25028400-25033600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:25028600-25032400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:25028600-25032800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:25028600-25033000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:25028600-25033200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:25028600-25033600	Weak transcription	Dnd41	blood
18	chr6:25028600-25034400	Weak transcription	Fetal Thymus	thymus
19	chr6:25028600-25034600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:25028800-25033600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:25029200-25032200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:25029600-25034600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:25030200-25033000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr6:25030600-25032200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:25030600-25032400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:25030600-25033200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr6:25030600-25033600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:25030800-25031400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:25030800-25031600	Strong transcription	Primary T cells fromperipheralblood	blood

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