Variant report

Variant	rs11961028
Chromosome Location	chr6:86389874-86389875
allele	A/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	MXI1	chr6:86386518-86390564	IMR90	lung:	n/a	n/a
2	HCFC1	chr6:86387002-86390095	Hela-S3	cervix:	n/a	n/a
3	IRF1	chr6:86386332-86390540	K562	blood:	n/a	chr6:86389992-86390012 chr6:86389999-86390016 chr6:86390000-86390011 chr6:86388505-86388519 chr6:86390001-86390012 chr6:86389999-86390011 chr6:86389998-86390011
4	CHD1	chr6:86384686-86390291	IMR90	lung:	n/a	n/a
5	MYC	chr6:86387903-86390199	MCF10A-Er-Src	breast:	n/a	chr6:86389008-86389017 chr6:86389007-86389018
6	KAP1	chr6:86387254-86390412	HEK293	kidney:	n/a	n/a
7	MXI1	chr6:86384658-86390661	SK-N-SH	brain:	n/a	n/a
8	MYC	chr6:86387833-86390243	MCF10A-Er-Src	breast:	n/a	chr6:86389008-86389017 chr6:86389007-86389018
9	MYC	chr6:86389837-86390598	K562	blood:	n/a	n/a
10	POLR2A	chr6:86381636-86390032	GM12891	blood:	n/a	n/a
11	FOS	chr6:86389640-86390007	MCF10A-Er-Src	breast:	n/a	n/a
12	RFX5	chr6:86389856-86390469	K562	blood:	n/a	n/a
13	SMC3	chr6:86388193-86389994	Hela-S3	cervix:	n/a	n/a
14	E2F4	chr6:86387982-86390060	MCF10A-Er-Src	breast:	n/a	chr6:86388725-86388736
15	CCNT2	chr6:86389827-86390033	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:86389006..86390560-chr6:86474592..86476523,2	K562	blood:
2	chr6:86338689..86357756-chr6:86378394..86390434,115	MCF-7	breast:
3	chr6:86360455..86373602-chr6:86382637..86391992,19	MCF-7	breast:
4	chr6:86287818..86291892-chr6:86385672..86390313,6	MCF-7	breast:
5	chr6:85471670..85475300-chr6:86386961..86389961,4	K562	blood:
6	chr6:86323280..86334231-chr6:86380512..86390230,24	K562	blood:
7	chr6:86302271..86307129-chr6:86385631..86390073,11	MCF-7	breast:
8	chr6:86246106..86247862-chr6:86386298..86390203,3	K562	blood:
9	chr6:31773748..31775519-chr6:86387939..86390447,2	MCF-7	breast:
10	chr6:86246140..86247926-chr6:86387829..86390203,2	K562	blood:
11	chr6:86389569..86391670-chr6:86458987..86460830,2	MCF-7	breast:
12	chr6:86300286..86310605-chr6:86384413..86390498,39	K562	blood:
13	chr6:86298349..86307534-chr6:86383938..86391964,31	K562	blood:

Variant related genes	Relation type
SNHG5	TF binding region
ENSG00000236016	Chromatin interaction
ENSG00000204392	Chromatin interaction
ENSG00000135316	Chromatin interaction
ENSG00000220563	Chromatin interaction
ENSG00000135317	Chromatin interaction
ENSG00000271793	Chromatin interaction
ENSG00000112837	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12524944	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12527778	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16876341	0.90[EUR][1000 genomes]
rs4626396	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4707208	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	nsv1028293	chr6:86353958-86778912	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
5	nsv538350	chr6:86353958-86778912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86385000-86390200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:86385000-86390400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:86385200-86390000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:86386000-86390200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:86386200-86390600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:86386800-86390000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:86386800-86390000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:86386800-86390200	Active TSS	NHLF	lung
9	chr6:86387000-86390200	Active TSS	GM12878-XiMat	blood
10	chr6:86387000-86390200	Active TSS	Hela-S3	cervix
11	chr6:86387200-86390200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:86387200-86390400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:86387200-86390600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:86387400-86390200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr6:86387600-86390200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:86387600-86390200	Active TSS	HSMM	muscle
17	chr6:86387600-86390200	Active TSS	K562	blood
18	chr6:86387800-86390600	Active TSS	A549	lung
19	chr6:86388000-86390000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:86388000-86390400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:86388000-86390400	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr6:86388000-86390400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr6:86388400-86390000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:86388400-86390400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr6:86388800-86390000	Flanking Active TSS	Fetal Thymus	thymus
26	chr6:86388800-86390200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:86388800-86390200	Flanking Active TSS	HMEC	breast
28	chr6:86388800-86390400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr6:86388800-86390600	Flanking Active TSS	Dnd41	blood
30	chr6:86389000-86390200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:86389000-86390200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:86389000-86390400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:86389000-86390400	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr6:86389000-86390400	Flanking Active TSS	HUVEC	blood vessel
35	chr6:86389200-86390000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:86389200-86390000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:86389200-86390000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr6:86389200-86390000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:86389200-86390000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:86389200-86390000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:86389200-86390000	Weak transcription	Gastric	stomach
42	chr6:86389200-86390200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:86389200-86390400	Flanking Active TSS	NHEK	skin
44	chr6:86389400-86390000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr6:86389400-86390000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:86389400-86390000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr6:86389400-86390000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr6:86389400-86390000	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr6:86389400-86390000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr6:86389400-86390200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links