Variant report

Variant	rs4959322
Chromosome Location	chr6:4974415-4974416
allele	C/G
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	NANOG	chr6:4974220-4974560	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA3	chr6:4974250-4974624	T-47D	breast:	n/a	n/a
3	NR2F2	chr6:4974284-4974695	MCF-7	breast:	n/a	n/a
4	TAF1	chr6:4974199-4974674	ECC-1	luminal epithelium:	n/a	n/a
5	TAF1	chr6:4974095-4974590	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr6:4974252-4974715	ECC-1	luminal epithelium:	n/a	chr6:4974283-4974293
7	POLR2A	chr6:4973955-4974709	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:4974163-4974688	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr6:4974138-4974510	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF7	chr6:4974127-4974588	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr6:4974342-4974601	MCF-7	breast:	n/a	n/a
12	JUND	chr6:4974383-4974531	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:4974208-4974457	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr6:4974161-4974505	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBP	chr6:4974203-4974599	H1-hESC	embryonic stem cell:	n/a	n/a
16	NFIC	chr6:4974251-4975210	ECC-1	luminal epithelium:	n/a	chr6:4974924-4974941 chr6:4974925-4974941
17	HCFC1	chr6:4974281-4974467	K562	blood:	n/a	n/a
18	UBTF	chr6:4974275-4974575	K562	blood:	n/a	n/a
19	TCF12	chr6:4974330-4974853	ECC-1	luminal epithelium:	n/a	n/a
20	NFIC	chr6:4974234-4975303	ECC-1	luminal epithelium:	n/a	chr6:4974924-4974941 chr6:4974925-4974941
21	CEBPB	chr6:4974146-4974607	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:4974196-4974544	H1-hESC	embryonic stem cell:	n/a	n/a
23	GABPA	chr6:4974261-4974593	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4973208..4976240-chr6:4987607..4989532,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000217030	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1246938	1.00[ASN][1000 genomes]
rs13197142	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17285799	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17285820	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34291130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953365	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4971400-4975000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:4972200-4974600	Weak transcription	Fetal Brain Female	brain
3	chr6:4973600-4975000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:4973600-4975000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:4973600-4975200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:4973600-4975800	Enhancers	Fetal Muscle Leg	muscle
7	chr6:4973800-4974600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:4973800-4974600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:4973800-4975000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:4973800-4975000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:4973800-4975200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:4973800-4975200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:4973800-4975200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:4973800-4975200	Enhancers	Adipose Nuclei	Adipose
15	chr6:4973800-4975400	Enhancers	Stomach Smooth Muscle	stomach
16	chr6:4973800-4975600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr6:4973800-4975600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:4973800-4975600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:4973800-4975600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:4973800-4975600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:4973800-4975600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:4973800-4975600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr6:4973800-4975600	Enhancers	Fetal Muscle Trunk	muscle
24	chr6:4973800-4975600	Enhancers	Psoas Muscle	Psoas
25	chr6:4973800-4975800	Enhancers	Fetal Stomach	stomach
26	chr6:4974000-4974800	Enhancers	Fetal Lung	lung
27	chr6:4974000-4974800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr6:4974000-4974800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr6:4974000-4975000	Enhancers	HSMMtube	muscle
30	chr6:4974000-4975400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:4974000-4976000	Enhancers	Fetal Brain Male	brain
32	chr6:4974200-4974600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:4974200-4974600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:4974200-4974600	Enhancers	Left Ventricle	heart
35	chr6:4974200-4975000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:4974200-4975400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:4974200-4975600	Enhancers	Rectal Smooth Muscle	rectum
38	chr6:4974400-4974600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:4974400-4974600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr6:4974400-4974600	Flanking Active TSS	Osteobl	bone
41	chr6:4974400-4974800	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr6:4974400-4975000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:4974400-4975000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:4974400-4975000	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr6:4974400-4975000	Bivalent Enhancer	HepG2	liver
46	chr6:4974400-4975200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:4974400-4975600	Enhancers	HUES6 Cell Line	embryonic stem cell

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