Variant report

Variant	rs609488
Chromosome Location	chr6:140261867-140261868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140256563..140258976-chr6:140261576..140263079,2	K562	blood:
2	chr6:140261744..140263602-chr6:140311555..140314319,2	MCF-7	breast:
3	chr6:140257717..140262130-chr6:140263178..140266087,5	K562	blood:
4	chr6:139867821..139870719-chr6:140261464..140264048,2	K562	blood:
5	chr6:140261253..140263387-chr6:140277092..140279215,2	MCF-7	breast:
6	chr6:140096649..140099517-chr6:140260643..140262599,2	K562	blood:
7	chr6:140240716..140243560-chr6:140261380..140263735,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1028469	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12525047	0.82[ASN][1000 genomes]
rs12526885	0.82[ASN][1000 genomes]
rs12663483	0.80[ASN][1000 genomes]
rs13204837	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1416289	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1953788	0.82[ASN][1000 genomes]
rs1953789	0.82[ASN][1000 genomes]
rs584995	0.83[AMR][1000 genomes]
rs586246	0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs587235	0.84[CHB][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs592056	0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs592440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs598498	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs603310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs607284	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs616279	0.83[CHB][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs618515	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs622216	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs647968	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs648510	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs650774	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs679849	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs680290	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs681235	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6926807	0.82[ASN][1000 genomes]
rs724061	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs7743374	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7763294	0.92[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs856646	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9373255	0.82[ASN][1000 genomes]
rs9376482	0.82[ASN][1000 genomes]
rs9385888	0.82[ASN][1000 genomes]
rs9389733	0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs9399298	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs9399299	0.80[ASN][1000 genomes]
rs9403134	0.86[CHB][hapmap];0.91[JPT][hapmap]

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	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	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
3	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
4	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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140255000-140262200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:140259200-140262800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:140259200-140263000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:140259200-140265600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:140259800-140262600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:140260000-140262600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:140260600-140262000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:140261000-140262000	Weak transcription	Fetal Brain Female	brain
9	chr6:140261000-140262200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:140261000-140262600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:140261000-140265400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:140261200-140262400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:140261200-140264200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:140261600-140262000	Enhancers	GM12878-XiMat	blood
15	chr6:140261600-140262800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:140261600-140262800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:140261600-140263600	Enhancers	HSMMtube	muscle
18	chr6:140261800-140262000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:140261800-140262000	Enhancers	Primary B cells from cord blood	blood
20	chr6:140261800-140262000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr6:140261800-140262000	Active TSS	Adipose Nuclei	Adipose
22	chr6:140261800-140262000	Enhancers	K562	blood
23	chr6:140261800-140262000	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr6:140261800-140262400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:140261800-140262600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:140261800-140262600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:140261800-140262600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr6:140261800-140262800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:140261800-140262800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:140261800-140262800	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:140261800-140262800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:140261800-140263400	Enhancers	HUVEC	blood vessel
33	chr6:140261800-140264000	Enhancers	HSMM	muscle
34	chr6:140261800-140265600	Enhancers	Osteobl	bone

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