Variant report

Variant	rs2499737
Chromosome Location	chr6:33883227-33883228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33881960..33884632-chr6:33890254..33892138,2	MCF-7	breast:
2	chr6:33878954..33881384-chr6:33881544..33883413,2	MCF-7	breast:
3	chr6:33868116..33871779-chr6:33880960..33883614,3	K562	blood:
4	chr6:33870279..33872339-chr6:33881420..33883614,2	K562	blood:
5	chr6:33875835..33878450-chr6:33882484..33884000,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITPR3-1	chr6:33882234-33885968	XLOC_005263
2	lnc-ITPR3-1	chr6:33882503-33885968	XLOC_005263
3	lnc-ITPR3-1	chr6:33882503-33885984	XLOC_005263
4	lnc-ITPR3-1	chr6:33882503-33885985	ENSG00000233183

No data

Variant related genes	Relation type
ENSG00000233183	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10807129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209273	1.00[AFR][1000 genomes]
rs1324579	0.99[EUR][1000 genomes]
rs1408503	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1535940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535943	0.88[EUR][1000 genomes]
rs1535944	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969843	0.95[EUR][1000 genomes]
rs2093907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147423	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147427	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147428	1.00[ASN][1000 genomes]
rs2181916	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477232	0.97[EUR][1000 genomes]
rs2477235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477236	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477237	0.97[EUR][1000 genomes]
rs2499681	0.83[EUR][1000 genomes]
rs4711364	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4711365	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713715	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713716	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713717	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713721	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457747	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6921366	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9296103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942506	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs942508	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942510	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942511	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv462899	chr6:33880480-33944014	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv602841	chr6:33880480-33944014	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33873000-33884000	Enhancers	Fetal Thymus	thymus
2	chr6:33873400-33883800	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:33874200-33889200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:33878000-33883600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr6:33879800-33883800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:33879800-33883800	Enhancers	Fetal Stomach	stomach
7	chr6:33880800-33883800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:33881000-33883800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:33881200-33884000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:33881400-33883400	Enhancers	Thymus	Thymus
11	chr6:33881400-33883600	Enhancers	Primary hematopoietic stem cells	blood
12	chr6:33881400-33883600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:33881400-33883800	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:33881600-33883400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr6:33881800-33883400	Enhancers	Primary B cells from cord blood	blood
16	chr6:33882000-33883400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:33882000-33883600	Enhancers	GM12878-XiMat	blood
18	chr6:33882200-33883400	Enhancers	Adipose Nuclei	Adipose
19	chr6:33882200-33883400	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr6:33882200-33883800	Enhancers	Fetal Muscle Leg	muscle
21	chr6:33882400-33883400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr6:33882600-33883800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:33882600-33883800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr6:33882800-33883800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:33882800-33884000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:33883000-33883400	Enhancers	Brain Germinal Matrix	brain
27	chr6:33883000-33883400	Enhancers	Fetal Muscle Trunk	muscle
28	chr6:33883000-33883400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr6:33883000-33883800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:33883000-33884000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:33883000-33884000	Enhancers	Primary T cells from cord blood	blood
32	chr6:33883000-33884000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr6:33883000-33884200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:33883200-33883600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr6:33883200-33883800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:33883200-33883800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:33883200-33889600	Weak transcription	Spleen	Spleen

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