Variant report

Variant	rs2817731
Chromosome Location	chr6:24913126-24913127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24904971..24907237-chr6:24911875..24914171,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2064524	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2207399	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493331	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747674	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2747675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747677	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2817727	0.84[ASN][1000 genomes]
rs2817733	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs932494	0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2817731	HERC3	trans	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24908600-24913200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
2	chr6:24908600-24913600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
3	chr6:24909000-24913400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
4	chr6:24909600-24913600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
5	chr6:24909600-24913600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
6	chr6:24909600-24914200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr6:24909600-24918000	Weak transcription	Dnd41	blood
8	chr6:24911600-24913400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
9	chr6:24911800-24914200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
10	chr6:24912000-24913600	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:24912000-24913800	Enhancers	Fetal Heart	heart
12	chr6:24912000-24916800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:24912200-24913200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:24912200-24913200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
15	chr6:24912200-24913400	Enhancers	Fetal Thymus	thymus
16	chr6:24912200-24914200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
17	chr6:24912200-24914200	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:24912400-24914200	Enhancers	Thymus	Thymus
19	chr6:24912400-24914800	Genic enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:24912400-24916400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:24912400-24917800	Weak transcription	Psoas Muscle	Psoas
22	chr6:24912400-24918200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:24912400-24918200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:24912400-24919200	Weak transcription	Left Ventricle	heart
25	chr6:24912400-24919600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:24912400-24926600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:24912600-24913400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:24912600-24915200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:24912600-24915400	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:24912600-24915800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:24912600-24916000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:24912600-24918000	Weak transcription	HSMMtube	muscle
33	chr6:24912600-24918800	Weak transcription	GM12878-XiMat	blood
34	chr6:24912600-24919400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:24912800-24913400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr6:24912800-24913600	Genic enhancers	Primary hematopoietic stem cells	blood
37	chr6:24912800-24914600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr6:24912800-24916800	Weak transcription	Right Ventricle	heart
39	chr6:24912800-24918200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:24913000-24913600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:24913000-24913800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr6:24913000-24918600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:24913000-24919000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:24913000-24919000	Weak transcription	Spleen	Spleen

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