Variant report

Variant	rs654917
Chromosome Location	chr6:140240886-140240887
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140240716..140243560-chr6:140261380..140263735,2	K562	blood:
2	chr6:140239712..140241213-chr6:140248206..140250375,2	K562	blood:
3	chr6:140238724..140241294-chr6:140241796..140244314,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2223966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs581559	0.99[ASN][1000 genomes]
rs590585	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs590587	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs592755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606159	0.99[ASN][1000 genomes]
rs608122	0.99[ASN][1000 genomes]
rs613274	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618471	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs627705	1.00[ASN][1000 genomes]
rs629778	0.96[ASN][1000 genomes]
rs632430	0.87[CHB][hapmap]
rs633026	0.99[ASN][1000 genomes]
rs661063	0.86[ASN][1000 genomes]
rs6904492	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7744208	0.85[JPT][hapmap]
rs7760148	0.85[JPT][hapmap]
rs9376477	0.85[JPT][hapmap]
rs9376478	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140227000-140247600	Weak transcription	Small Intestine	intestine
2	chr6:140238600-140242400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:140238600-140242400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:140239000-140241000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:140239000-140241800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:140239000-140242200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:140239200-140242200	Enhancers	K562	blood
8	chr6:140239200-140242400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:140239600-140241200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:140239600-140241200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:140239600-140241200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:140239800-140241000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:140239800-140241200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:140239800-140241200	Weak transcription	Fetal Lung	lung
15	chr6:140239800-140244800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:140239800-140246400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:140239800-140251600	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:140240000-140248000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:140240200-140241600	Weak transcription	Fetal Brain Male	brain
20	chr6:140240200-140241800	Enhancers	Fetal Heart	heart
21	chr6:140240400-140241000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:140240400-140241400	Enhancers	Left Ventricle	heart
23	chr6:140240400-140241400	Enhancers	Right Atrium	heart
24	chr6:140240400-140241800	Enhancers	Placenta	Placenta
25	chr6:140240400-140242000	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:140240400-140242200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr6:140240400-140242200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr6:140240600-140241000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr6:140240600-140241200	Enhancers	Primary hematopoietic stem cells	blood
30	chr6:140240600-140241200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:140240600-140242400	Enhancers	Brain Germinal Matrix	brain
32	chr6:140240800-140241400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr6:140240800-140241400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:140240800-140241400	Enhancers	Fetal Thymus	thymus
35	chr6:140240800-140241600	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr6:140240800-140241800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:140240800-140242400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:140240800-140242400	Weak transcription	Rectal Mucosa Donor 29	rectum

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