Variant report

Variant	rs640380
Chromosome Location	chr6:24938201-24938202
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24720932..24722998-chr6:24938200..24939892,2	K562	blood:
2	chr6:24937346..24939833-chr6:25024037..25025919,2	K562	blood:

Variant related genes	Relation type
ENSG00000220517	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12202529	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216261	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626145	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16889797	0.87[EUR][1000 genomes]
rs16889835	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1753511	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1813711	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs216256	0.93[ASN][1000 genomes]
rs216257	0.86[ASN][1000 genomes]
rs216258	0.83[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs216260	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs216261	1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs216262	0.90[ASN][1000 genomes]
rs370748	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs386511	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs388071	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs413203	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413610	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs415025	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs419288	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs421817	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431796	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs432593	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs495157	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs62402043	0.89[EUR][1000 genomes]
rs628794	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs640845	0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644722	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs644748	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685008	0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7742242	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356949	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379698	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24936200-24939000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr6:24936200-24941200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:24936400-24938600	Enhancers	Fetal Thymus	thymus
4	chr6:24936400-24938800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr6:24937000-24938800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr6:24937000-24939000	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr6:24937000-24939000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr6:24937000-24942400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:24937200-24938600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:24937200-24938600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr6:24937200-24938600	Enhancers	Spleen	Spleen
12	chr6:24937200-24939600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:24937200-24944200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:24937400-24938800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:24937400-24939400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:24937400-24939800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:24937600-24938600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:24937600-24940800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:24937600-24941200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:24937600-24942600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:24937600-24943800	Weak transcription	Dnd41	blood
22	chr6:24937800-24938400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:24937800-24938600	Enhancers	Thymus	Thymus
24	chr6:24937800-24939800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr6:24938000-24938400	Enhancers	Primary B cells from cord blood	blood
26	chr6:24938000-24938400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr6:24938000-24938800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:24938000-24939600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:24938000-24940200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr6:24938200-24938600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:24938200-24938600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr6:24938200-24940000	Enhancers	GM12878-XiMat	blood
33	chr6:24938200-24940400	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:24938200-24941800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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