Variant report

Variant	rs1246988
Chromosome Location	chr6:5005300-5005301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr6:5003560-5005590	IMR90	lung:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
2	JUN	chr6:5003441-5005330	K562	blood:	n/a	n/a
3	POLR2A	chr6:5003577-5005411	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr6:5003523-5005327	HepG2	liver:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5004268..5006268-chr6:5028632..5030855,2	K562	blood:
2	chr6:5004308..5006000-chr6:5030652..5032441,2	K562	blood:

Variant related genes	Relation type
RPP40	TF binding region
ENSG00000272142	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10900964	0.91[EUR][1000 genomes]
rs1246982	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1246985	0.87[ASN][1000 genomes]
rs1246989	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1246990	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246992	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1271970	0.87[ASN][1000 genomes]
rs1615873	0.84[ASN][1000 genomes]
rs1617590	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1749144	0.84[ASN][1000 genomes]
rs1749158	0.84[ASN][1000 genomes]
rs396839	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs412444	0.93[ASN][1000 genomes]
rs431060	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs443167	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs563589	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707966	0.93[ASN][1000 genomes]
rs728151	0.87[ASN][1000 genomes]
rs7744457	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5004600-5014000	Weak transcription	Lung	lung
2	chr6:5004800-5005400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr6:5004800-5006200	Weak transcription	Gastric	stomach
4	chr6:5004800-5012200	Weak transcription	Ovary	ovary
5	chr6:5004800-5012800	Weak transcription	Aorta	Aorta
6	chr6:5004800-5013000	Weak transcription	Esophagus	oesophagus
7	chr6:5005000-5005400	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:5005000-5006400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:5005000-5008000	Weak transcription	Spleen	Spleen
10	chr6:5005200-5005400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:5005200-5005400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:5005200-5005400	Enhancers	Dnd41	blood
13	chr6:5005200-5005400	Enhancers	HepG2	liver
14	chr6:5005200-5005400	Active TSS	NHDF-Ad	bronchial
15	chr6:5005200-5006400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:5005200-5006600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:5005200-5006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:5005200-5006600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:5005200-5006800	Weak transcription	Fetal Lung	lung
20	chr6:5005200-5007400	Weak transcription	Fetal Kidney	kidney
21	chr6:5005200-5007800	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:5005200-5007800	Weak transcription	K562	blood
23	chr6:5005200-5008000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:5005200-5008000	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:5005200-5008000	Weak transcription	Fetal Thymus	thymus
26	chr6:5005200-5012400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:5005200-5013000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:5005200-5013000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:5005200-5013200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:5005200-5014200	Weak transcription	Primary T cells from cord blood	blood
31	chr6:5005200-5017000	Weak transcription	Primary B cells from cord blood	blood
32	chr6:5005200-5025800	Weak transcription	Primary B cells from peripheral blood	blood

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