Variant report

Variant	rs1953789
Chromosome Location	chr6:140264321-140264322
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:140257717..140262130-chr6:140263178..140266087,5	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1028469	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12175776	0.82[EUR][1000 genomes]
rs12525047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663217	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12663483	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665399	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13194747	0.87[EUR][1000 genomes]
rs13194827	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13204837	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1416289	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1933742	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1953788	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586246	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs587235	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs592056	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs598498	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs609488	0.82[ASN][1000 genomes]
rs616279	0.99[ASN][1000 genomes]
rs618515	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs622216	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62429515	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62429516	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62429517	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs647968	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67013338	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679849	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs680290	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs681235	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6926807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928433	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724061	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7743656	0.90[ASN][1000 genomes]
rs856646	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9373255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376482	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376485	0.88[EUR][1000 genomes]
rs9385888	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389733	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399299	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9403134	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403135	0.88[EUR][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	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:55 , 50 per page) page: 1 2

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	chr6:140261800-140265600	Enhancers	Osteobl	bone
4	chr6:140262000-140265600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:140262000-140265800	Enhancers	NHDF-Ad	bronchial
6	chr6:140262600-140264600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:140262600-140265400	Enhancers	Adipose Nuclei	Adipose
8	chr6:140262600-140265800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:140262800-140266200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:140262800-140266600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:140263000-140265200	Enhancers	Fetal Lung	lung
12	chr6:140263200-140264400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:140263200-140264400	Enhancers	K562	blood
14	chr6:140263200-140265600	Enhancers	NHLF	lung
15	chr6:140263400-140265600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:140263400-140265600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:140263400-140265800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr6:140263600-140264600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:140263600-140264800	Enhancers	Fetal Heart	heart
20	chr6:140263600-140264800	Enhancers	Fetal Stomach	stomach
21	chr6:140263600-140265400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:140263600-140265600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:140263600-140265600	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr6:140263600-140265600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:140263600-140265600	Enhancers	Fetal Kidney	kidney
26	chr6:140263600-140265600	Enhancers	Hela-S3	cervix
27	chr6:140263800-140264400	Genic enhancers	Aorta	Aorta
28	chr6:140263800-140264400	Enhancers	Ovary	ovary
29	chr6:140263800-140264600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:140263800-140264800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:140263800-140265000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr6:140263800-140265200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:140263800-140265200	Enhancers	Rectal Smooth Muscle	rectum
34	chr6:140263800-140265200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr6:140263800-140265600	Enhancers	HUVEC	blood vessel
36	chr6:140263800-140265800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:140263800-140266000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:140264000-140264400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:140264000-140265200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr6:140264000-140265200	Enhancers	Placenta Amnion	Placenta Amnion
41	chr6:140264000-140265200	Enhancers	HSMMtube	muscle
42	chr6:140264000-140265400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:140264000-140265400	Enhancers	Colon Smooth Muscle	Colon
44	chr6:140264000-140265400	Enhancers	NH-A	brain
45	chr6:140264200-140264400	Enhancers	HSMM	muscle
46	chr6:140264200-140264600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:140264200-140264600	Enhancers	A549	lung
48	chr6:140264200-140264800	Enhancers	Fetal Intestine Small	intestine
49	chr6:140264200-140265000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:140264200-140265000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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