Variant report

Variant	rs1028469
Chromosome Location	chr6:140263343-140263344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140257717..140262130-chr6:140263178..140266087,5	K562	blood:
2	chr6:140261744..140263602-chr6:140311555..140314319,2	MCF-7	breast:
3	chr6:139867821..139870719-chr6:140261464..140264048,2	K562	blood:
4	chr6:139866369..139869321-chr6:140262548..140264111,2	K562	blood:
5	chr6:140261253..140263387-chr6:140277092..140279215,2	MCF-7	breast:
6	chr6:140240716..140243560-chr6:140261380..140263735,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12525047	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12526885	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12663217	0.95[ASN][1000 genomes]
rs12663483	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12665399	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13194827	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13204837	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1416289	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1933742	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1953788	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1953789	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs586246	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587235	0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592440	0.84[EUR][1000 genomes]
rs598498	0.85[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs599378	0.81[AMR][1000 genomes]
rs603310	0.84[EUR][1000 genomes]
rs607284	0.84[EUR][1000 genomes]
rs609488	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs616279	0.89[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622216	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62429515	0.98[ASN][1000 genomes]
rs62429516	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62429517	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs647968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648510	0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs650774	0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs67013338	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs679849	0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680290	0.85[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681235	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926807	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6928433	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs724061	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7743656	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs856646	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373255	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9376482	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9385888	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9389733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9399298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9399299	0.99[ASN][1000 genomes]
rs9403134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9495636	0.88[YRI][hapmap]
rs9495641	0.88[YRI][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1028469	HIVEP2	cis	parietal	SCAN
rs1028469	CITED2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140259200-140265600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:140261000-140265400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:140261200-140264200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:140261600-140263600	Enhancers	HSMMtube	muscle
5	chr6:140261800-140263400	Enhancers	HUVEC	blood vessel
6	chr6:140261800-140264000	Enhancers	HSMM	muscle
7	chr6:140261800-140265600	Enhancers	Osteobl	bone
8	chr6:140262000-140264200	Enhancers	Placenta	Placenta
9	chr6:140262000-140265600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:140262000-140265800	Enhancers	NHDF-Ad	bronchial
11	chr6:140262200-140263600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr6:140262200-140263600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:140262200-140264000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:140262200-140264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:140262400-140263400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:140262400-140263600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:140262400-140263600	Weak transcription	Aorta	Aorta
18	chr6:140262400-140263600	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:140262400-140264000	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:140262600-140263400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:140262600-140263600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:140262600-140263600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:140262600-140263600	Weak transcription	Hela-S3	cervix
24	chr6:140262600-140263800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:140262600-140263800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:140262600-140264600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:140262600-140265400	Enhancers	Adipose Nuclei	Adipose
28	chr6:140262600-140265800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:140262800-140263600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr6:140262800-140263600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:140262800-140263800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:140262800-140263800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:140262800-140263800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:140262800-140263800	Weak transcription	Ovary	ovary
35	chr6:140262800-140263800	Weak transcription	Right Ventricle	heart
36	chr6:140262800-140264000	Weak transcription	NH-A	brain
37	chr6:140262800-140264200	Weak transcription	Fetal Intestine Small	intestine
38	chr6:140262800-140266200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:140262800-140266600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:140263000-140263400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:140263000-140265200	Enhancers	Fetal Lung	lung
42	chr6:140263200-140263600	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr6:140263200-140264200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:140263200-140264400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:140263200-140264400	Enhancers	K562	blood
46	chr6:140263200-140265600	Enhancers	NHLF	lung

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