Variant report

Variant	rs2295663
Chromosome Location	chr6:31669295-31669296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:31668587-31672641	K562	blood:	n/a	n/a
2	MXI1	chr6:31669231-31671652	SK-N-SH	brain:	n/a	chr6:31669547-31669562 chr6:31669800-31669809
3	JUND	chr6:31669240-31671573	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31668602..31672513-chr6:31741310..31744822,4	MCF-7	breast:
2	chr6:31668218..31672980-chr6:31695553..31699160,10	MCF-7	breast:
3	chr6:31668227..31672274-chr6:31683898..31689448,8	MCF-7	breast:
4	chr6:31668441..31672326-chr6:31702683..31707609,7	MCF-7	breast:
5	chr6:31669236..31670926-chr6:31800796..31802801,2	MCF-7	breast:
6	chr6:31667922..31671961-chr6:31761581..31764967,5	MCF-7	breast:
7	chr6:31654373..31658459-chr6:31668305..31672590,5	MCF-7	breast:
8	chr6:31626203..31628838-chr6:31668692..31672480,4	MCF-7	breast:
9	chr6:31631824..31634552-chr6:31668867..31671892,6	MCF-7	breast:
10	chr6:31668504..31670633-chr6:31865302..31866839,2	K562	blood:
11	chr6:31655444..31658089-chr6:31668201..31670879,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4646	TF binding region
ENSG00000204396	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000204420	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000204394	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2272592	0.84[ASN][1000 genomes]
rs2280801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28732150	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28732154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28732157	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28732158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131384	0.87[ASN][1000 genomes]
rs3993757	0.88[ASN][1000 genomes]
rs9368699	1.00[AMR][1000 genomes]
rs9378164	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380266	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9391731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9404941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
12	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
13	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
14	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2295663	C6orf48	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31649600-31669400	Weak transcription	HMEC	breast
2	chr6:31658800-31670000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31659000-31669400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:31659800-31669400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:31663200-31669400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:31663200-31669600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:31663200-31669800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:31664600-31669400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:31664800-31669600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:31665000-31669400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:31665000-31669400	Weak transcription	Small Intestine	intestine
12	chr6:31665400-31669600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:31665600-31669400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:31665800-31669400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:31666600-31669800	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr6:31667800-31669400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:31667800-31669400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:31667800-31669400	Genic enhancers	Duodenum Mucosa	Duodenum
19	chr6:31667800-31669600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:31668200-31669600	Enhancers	Fetal Intestine Large	intestine
21	chr6:31668400-31669400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:31668400-31669600	Genic enhancers	Fetal Intestine Small	intestine
23	chr6:31668400-31669800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:31668600-31669400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:31668600-31669400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr6:31668600-31669400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:31668600-31669400	Enhancers	Brain Angular Gyrus	brain
28	chr6:31668600-31669400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
29	chr6:31668600-31669400	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr6:31668600-31669400	Enhancers	Pancreas	Pancrea
31	chr6:31668600-31669600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:31668600-31669600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:31668600-31669600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr6:31668600-31669600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:31668600-31669600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr6:31668600-31669600	Enhancers	Fetal Lung	lung
37	chr6:31668600-31669600	Genic enhancers	Fetal Muscle Leg	muscle
38	chr6:31668600-31669600	Genic enhancers	Fetal Stomach	stomach
39	chr6:31668600-31669600	Enhancers	Gastric	stomach
40	chr6:31668600-31669600	Genic enhancers	Stomach Mucosa	stomach
41	chr6:31668600-31669800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:31668600-31669800	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr6:31668600-31669800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:31668600-31669800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:31668600-31669800	Enhancers	Liver	Liver
46	chr6:31668600-31669800	Genic enhancers	Placenta	Placenta
47	chr6:31668600-31669800	Genic enhancers	Fetal Thymus	thymus
48	chr6:31668600-31669800	Enhancers	Right Atrium	heart
49	chr6:31668600-31669800	Enhancers	A549	lung
50	chr6:31668600-31669800	Transcr. at gene 5' and 3'	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links