Variant report

Variant	rs2038139
Chromosome Location	chr6:24645420-24645421
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24644992..24647314-chr6:24719656..24721157,2	MCF-7	breast:
2	chr6:24645396..24648521-chr6:24658092..24661192,3	K562	blood:
3	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:
4	chr6:24645396..24648552-chr6:24658188..24661192,4	K562	blood:

Variant related genes	Relation type
ENSG00000111802	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1047782	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs1555089	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555090	0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038135	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038136	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038137	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2038138	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143341	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2143342	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2179515	0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2206525	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2223590	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235677	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328846	0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712835	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456622	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456624	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903205	0.90[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903738	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906247	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917244	0.80[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap]
rs6917660	0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6923143	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923652	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923845	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923867	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938069	0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6938411	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761100	0.80[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs761101	0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741572	0.97[ASN][1000 genomes]
rs7751357	0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755563	0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7755983	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7759417	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7759592	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7759747	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760198	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356940	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356941	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358777	0.91[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358778	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358779	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9358780	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358783	0.89[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358784	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366573	0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366574	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366575	0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366576	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379676	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379678	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393568	0.81[EUR][1000 genomes]
rs9393569	0.81[AMR][1000 genomes]
rs9393570	0.90[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393571	0.89[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467244	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467245	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467249	0.89[AMR][1000 genomes];0.83[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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24642400-24645600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:24643600-24647000	Active TSS	Fetal Brain Female	brain
3	chr6:24644000-24646800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:24644000-24647000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:24644200-24645600	Bivalent Enhancer	HepG2	liver
6	chr6:24644200-24647000	Active TSS	Brain Anterior Caudate	brain
7	chr6:24644400-24645600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:24644400-24645800	Weak transcription	Gastric	stomach
9	chr6:24644600-24645600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:24644600-24645800	Active TSS	Fetal Brain Male	brain
11	chr6:24644600-24645800	Weak transcription	Lung	lung
12	chr6:24644800-24645600	Flanking Active TSS	A549	lung
13	chr6:24645200-24645600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
14	chr6:24645400-24645600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:24645400-24645600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:24645400-24645600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
17	chr6:24645400-24645600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
18	chr6:24645400-24645600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr6:24645400-24645600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
20	chr6:24645400-24645600	Flanking Active TSS	Hela-S3	cervix
21	chr6:24645400-24645800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:24645400-24645800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:24645400-24646000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:24645400-24646000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
25	chr6:24645400-24646000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:24645400-24647000	Active TSS	Brain Angular Gyrus	brain

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