Variant report

Variant	rs28732150
Chromosome Location	chr6:31583224-31583225
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	SPI1	chr6:31582605-31583267	HL-60	blood:	n/a	chr6:31582944-31582957 chr6:31582946-31582955 chr6:31583252-31583259
2	MTA3	chr6:31582754-31584475	GM12878	blood:	n/a	n/a
3	ELF1	chr6:31582761-31583324	K562	blood:	n/a	n/a
4	POLR2A	chr6:31582725-31583319	HL-60	blood:	n/a	n/a
5	POLR2A	chr6:31583020-31584009	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31513771..31519008-chr6:31582734..31585702,4	K562	blood:
2	chr6:31539772..31542619-chr6:31581316..31584667,3	K562	blood:
3	chr6:31578073..31580095-chr6:31581694..31583880,2	MCF-7	breast:
4	chr6:31510094..31511838-chr6:31582401..31584650,2	K562	blood:
5	chr6:31513234..31515924-chr6:31582326..31585070,2	K562	blood:

Variant related genes	Relation type
UQCRHP1	TF binding region
AIF1	TF binding region
ENSG00000204498	Chromatin interaction
ENSG00000226979	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000230622	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000234006	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2280801	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2295663	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28732148	0.92[EUR][1000 genomes]
rs28732154	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28732157	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28732158	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28895016	0.95[EUR][1000 genomes]
rs3993757	0.93[ASN][1000 genomes]
rs6920486	0.89[EUR][1000 genomes]
rs9348876	0.92[EUR][1000 genomes]
rs9368699	1.00[AMR][1000 genomes]
rs9378164	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9378200	0.91[EUR][1000 genomes]
rs9380266	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391731	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9404941	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv462871	chr6:31575276-31632134	Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
15	nsv601942	chr6:31575276-31632134	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28732150	C6orf48	cis	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31581200-31583400	Enhancers	Fetal Intestine Small	intestine
2	chr6:31581400-31583400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr6:31581400-31585200	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:31581600-31583400	Flanking Active TSS	HepG2	liver
5	chr6:31581800-31584400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:31582000-31584000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:31582000-31584200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:31582000-31584200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr6:31582000-31584800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr6:31582000-31585200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:31582200-31583600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:31582200-31583600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:31582200-31584200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:31582200-31584200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:31582200-31584400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:31582200-31584400	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr6:31582200-31584400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr6:31582200-31585000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:31582200-31587800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:31582400-31583600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:31582600-31583600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:31582600-31583800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:31582600-31584000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:31582600-31584400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:31582600-31584400	Flanking Active TSS	Fetal Thymus	thymus
26	chr6:31582600-31584800	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr6:31582800-31583400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:31582800-31583400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:31582800-31583800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:31582800-31584000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:31582800-31584000	Enhancers	Fetal Lung	lung
32	chr6:31582800-31584200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr6:31582800-31584200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr6:31582800-31584400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr6:31583000-31583400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:31583000-31583400	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr6:31583000-31583600	Active TSS	Primary monocytes fromperipheralblood	blood
38	chr6:31583000-31583600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:31583000-31583600	Active TSS	Stomach Smooth Muscle	stomach
40	chr6:31583000-31584200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:31583000-31584200	Active TSS	Adipose Nuclei	Adipose
42	chr6:31583000-31584200	Active TSS	Fetal Muscle Trunk	muscle
43	chr6:31583000-31584400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr6:31583000-31584400	Active TSS	Brain Substantia Nigra	brain
45	chr6:31583000-31584400	Active TSS	Fetal Muscle Leg	muscle
46	chr6:31583000-31584600	Active TSS	Placenta	Placenta
47	chr6:31583000-31584800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr6:31583000-31584800	Flanking Active TSS	Dnd41	blood
49	chr6:31583000-31585000	Enhancers	K562	blood
50	chr6:31583000-31587200	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links