Variant report

Variant	rs2747678
Chromosome Location	chr6:24888955-24888956
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24886932..24889489-chr6:24891782..24893899,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10946732	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946735	0.87[CEU][hapmap]
rs12111413	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192978	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211772	1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215106	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220782	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17671350	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207400	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2207401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747679	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35158242	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35250553	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35953835	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61595405	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456637	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918387	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918511	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555168	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24855200-24895000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
2	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
3	chr6:24878400-24899800	Weak transcription	Thymus	Thymus
4	chr6:24880000-24889200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:24881200-24898400	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr6:24881400-24895400	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr6:24881800-24891000	Weak transcription	Psoas Muscle	Psoas
8	chr6:24882400-24904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:24882600-24899200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:24884000-24889600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:24884200-24891000	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:24884200-24899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:24885600-24891200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr6:24885600-24896600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:24885800-24890000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr6:24886400-24889400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr6:24886600-24895000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:24886800-24889400	Enhancers	Fetal Heart	heart
20	chr6:24886800-24889600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:24887000-24889600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:24887000-24890200	Genic enhancers	Primary B cells from cord blood	blood
23	chr6:24887000-24894000	Weak transcription	Fetal Thymus	thymus
24	chr6:24887000-24900000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:24887200-24889200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:24887200-24889400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr6:24887200-24889600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:24887400-24889600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:24887400-24889600	Enhancers	HSMMtube	muscle
30	chr6:24887400-24889800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:24887400-24897400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:24887400-24898000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:24887600-24889600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:24887800-24889000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:24887800-24889400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:24887800-24889400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:24887800-24890800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:24887800-24891000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr6:24888000-24889400	Enhancers	Brain Anterior Caudate	brain
40	chr6:24888000-24889800	Enhancers	Brain Germinal Matrix	brain
41	chr6:24888200-24889000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:24888200-24889400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr6:24888200-24890000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:24888200-24892600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr6:24888200-24897400	Weak transcription	Fetal Brain Female	brain
46	chr6:24888400-24889000	Enhancers	GM12878-XiMat	blood
47	chr6:24888400-24889200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:24888400-24889800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:24888400-24891400	Weak transcription	NHDF-Ad	bronchial
50	chr6:24888600-24889000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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