Variant report

Variant	rs1987244
Chromosome Location	chr6:26298538-26298539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26295929..26298727-chr6:27833801..27835799,2	K562	blood:
2	chr6:26297237..26299588-chr6:26519952..26522018,2	K562	blood:
3	chr6:26298389..26300279-chr6:26305818..26308233,2	MCF-7	breast:
4	chr6:26298226..26302265-chr6:26302450..26306372,5	MCF-7	breast:
5	chr6:26295520..26298937-chr6:26299189..26303889,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST1H2BI-2	chr6:26296251-26298574	NONHSAT108254

Variant related genes	Relation type
ENSG00000184357	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1053860	0.84[ASN][1000 genomes]
rs10946810	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12525187	0.81[EUR][1000 genomes]
rs12660432	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12661552	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665035	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13210340	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17608582	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1883213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393649	0.90[EUR][1000 genomes]
rs2893820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2893842	0.90[EUR][1000 genomes]
rs2893843	0.81[EUR][1000 genomes]
rs3778279	0.84[ASN][1000 genomes]
rs4412193	0.81[EUR][1000 genomes]
rs56763414	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61324092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61534839	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62394764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62394768	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62394769	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6456713	0.84[ASN][1000 genomes]
rs6918325	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6930616	0.81[EUR][1000 genomes]
rs6932584	0.84[ASN][1000 genomes]
rs6932727	0.84[ASN][1000 genomes]
rs6933139	0.84[ASN][1000 genomes]
rs725575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755741	0.90[EUR][1000 genomes]
rs9357005	0.81[EUR][1000 genomes]
rs9358914	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9358916	0.82[EUR][1000 genomes]
rs9358918	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9358920	0.83[EUR][1000 genomes]
rs9358924	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9358925	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9358926	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9358927	0.81[EUR][1000 genomes]
rs9366648	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366650	0.81[EUR][1000 genomes]
rs9379842	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379844	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379845	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393691	0.82[EUR][1000 genomes]
rs9393696	0.83[EUR][1000 genomes]
rs9393697	0.83[EUR][1000 genomes]
rs9393700	0.88[ASN][1000 genomes]
rs989133	0.91[EUR][1000 genomes]
rs994379	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
7	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
8	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
9	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
10	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases
11	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26294600-26299200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:26294800-26299200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr6:26295000-26298800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:26296400-26301000	Weak transcription	Thymus	Thymus
5	chr6:26296400-26301200	Weak transcription	GM12878-XiMat	blood
6	chr6:26297400-26299400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:26297400-26299400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:26297600-26299000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:26297600-26299400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:26297600-26299400	Weak transcription	NHEK	skin
11	chr6:26297600-26299400	Weak transcription	Osteobl	bone
12	chr6:26297600-26300200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:26297600-26300200	Weak transcription	NHDF-Ad	bronchial
14	chr6:26297600-26304400	Weak transcription	NHLF	lung
15	chr6:26297800-26300000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:26297800-26303200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:26297800-26303200	Weak transcription	HepG2	liver
18	chr6:26297800-26304800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:26297800-26305000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:26298000-26305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:26298200-26299000	Enhancers	K562	blood

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