Variant report

Variant	rs2239709
Chromosome Location	chr6:31507447-31507448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31505570-31507667	K562	blood:	n/a	n/a
2	POLR2A	chr6:31505026-31508472	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:31507034-31508750	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:31505301-31507731	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr6:31507286-31507585	K562	blood:	n/a	n/a
6	POLR2A	chr6:31507201-31507814	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:31505312-31508500	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:31506089-31508478	HepG2	liver:	n/a	n/a
9	HEY1	chr6:31506024-31508418	K562	blood:	n/a	n/a
10	POLR2A	chr6:31506295-31508505	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:31505819-31511508	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr6:31507021-31507533	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:31507238-31507739	K562	blood:	n/a	n/a
14	POLR2A	chr6:31506246-31507453	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31507433-31507483	AG09309	skin:	n/a
2	chr6:31507433-31507483	MCF-7	breast:	n/a
3	chr6:31507433-31507483	Caco-2	colon:	n/a
4	chr6:31507433-31507483	HEK293	kidney:	embryo
5	chr6:31507433-31507483	Hela-S3	cervix:	n/a
6	chr6:31507433-31507483	ovcar-3	ovarian:	n/a
7	chr6:31507433-31507483	SK-N-SH_RA	brain:	n/a
8	chr6:31507433-31507483	GM12892	blood:	n/a
9	chr6:31507433-31507483	ECC-1	luminal epithelium:	n/a
10	chr6:31507433-31507483	GM19239	blood:	n/a
11	chr6:31507433-31507483	HEEpiC	esophagus:	n/a
12	chr6:31507433-31507483	BE2_C	brain:	n/a
13	chr6:31507433-31507483	RPTEC	kidney:	n/a
14	chr6:31507433-31507483	SAEC	small airway:	n/a
15	chr6:31507433-31507483	HAEpiC	amniotic membrane:	n/a
16	chr6:31507433-31507483	HUVEC	blood vessel:	n/a
17	chr6:31507433-31507483	NH-A	brain:	n/a
18	chr6:31507433-31507483	HMEC	breast:	n/a
19	chr6:31507433-31507483	HL-60	blood:	n/a
20	chr6:31507433-31507483	H1-hESC	embryonic stem cell:	embryo
21	chr6:31507433-31507483	BJ	skin:	n/a
22	chr6:31507433-31507483	U87	brain:	n/a
23	chr6:31507433-31507483	GM06990	blood:	n/a
24	chr6:31507433-31507483	PANC-1	pancreas:	n/a
25	chr6:31507433-31507483	AG10803	skin:	n/a
26	chr6:31507433-31507483	SKMC	muscle:	n/a
27	chr6:31507433-31507483	AG04449	skin:	fetal
28	chr6:31507433-31507483	Hepatocyte	liver:	n/a
29	chr6:31507433-31507483	PFSK-1	brain:	n/a
30	chr6:31507433-31507483	IMR90	lung:	fetal
31	chr6:31507433-31507483	NB4	blood:	n/a
32	chr6:31507433-31507483	HRCEpiC	kidney:	n/a
33	chr6:31507433-31507483	NHDF-neo	bronchial:	n/a
34	chr6:31507433-31507483	SK-N-MC	brain:	n/a
35	chr6:31507433-31507483	NT2-D1	testis:	n/a
36	chr6:31507433-31507483	GM12891	blood:	n/a
37	chr6:31507433-31507483	AG09319	gingival:	n/a
38	chr6:31507433-31507483	HIPEpiC	eye:	n/a
39	chr6:31507433-31507483	T-47D	breast:	n/a
40	chr6:31507433-31507483	AG04450	lung:	fetal
41	chr6:31507433-31507483	K562	blood:	n/a
42	chr6:31507433-31507483	GM12878	blood:	n/a
43	chr6:31507433-31507483	HCM	heart:	n/a
44	chr6:31507433-31507483	HepG2	liver:	n/a
45	chr6:31507433-31507483	HCPEpiC	choroid plexus:	n/a
46	chr6:31507433-31507483	HRPEpiC	eye:	n/a
47	chr6:31507433-31507483	HCT-116	colon:	n/a
48	chr6:31507433-31507483	CMK	blood:	n/a
49	chr6:31507433-31507483	Jurkat	blood:	n/a
50	chr6:31507433-31507483	A549	lung:	n/a

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31507082..31511713-chr6:31583957..31591905,17	MCF-7	breast:
2	chr6:31506561..31512642-chr6:31697539..31702106,5	K562	blood:
3	chr6:31506496..31512275-chr6:31630248..31634828,11	K562	blood:
4	chr6:31459710..31467567-chr6:31506191..31511027,18	MCF-7	breast:
5	chr6:31504619..31508588-chr6:31538806..31541615,4	K562	blood:
6	chr6:31506740..31512488-chr6:31586502..31592966,30	K562	blood:
7	chr6:31507082..31510843-chr6:31599707..31603450,4	K562	blood:
8	chr6:31506595..31512441-chr6:31585525..31590767,30	K562	blood:
9	chr6:31506529..31508833-chr6:31606767..31610616,4	K562	blood:
10	chr6:31507205..31511686-chr6:31618024..31622039,13	K562	blood:
11	chr6:31458384..31468965-chr6:31503613..31512721,28	K562	blood:
12	chr6:31506998..31509094-chr6:31864561..31866443,2	MCF-7	breast:
13	chr6:31507406..31516955-chr6:31615847..31623354,26	K562	blood:
14	chr6:31505350..31512312-chr6:31630543..31635379,11	K562	blood:
15	chr6:31505549..31508168-chr6:31560722..31562471,2	K562	blood:
16	chr6:31506029..31511048-chr6:31626239..31630287,7	MCF-7	breast:
17	chr6:31507058..31511692-chr6:31586700..31590601,11	MCF-7	breast:
18	chr6:31460486..31468205-chr6:31503942..31512721,23	K562	blood:
19	chr6:31504619..31510971-chr6:31539361..31543067,6	K562	blood:

No data

Variant related genes	Relation type
DDX39B-AS1	TF binding region
DDX39B	TF binding region
SNORD117	TF binding region
DDX39B	CpG island
SNORD117	CpG island
DDX39B-AS1	CpG island
ENSG00000201207	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204475	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000226979	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000200816	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000204438	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1055385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2071595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3219184	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68092383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847209	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv1018463	chr6:31337336-31525275	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
13	nsv538189	chr6:31337336-31525275	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
14	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
15	esv2757162	chr6:31353329-31542308	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
16	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
17	nsv432877	chr6:31412961-31528690	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
18	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
19	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31496800-31507800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:31497600-31507600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:31497600-31508000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:31498200-31507600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:31503800-31508200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
6	chr6:31504400-31507800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:31504400-31508400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:31505400-31508000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:31505400-31508400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
10	chr6:31505600-31507800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:31505600-31508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:31505600-31508800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:31506000-31507600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:31506000-31507800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr6:31506000-31507800	Genic enhancers	Brain Anterior Caudate	brain
16	chr6:31506000-31507800	Genic enhancers	Brain Hippocampus Middle	brain
17	chr6:31506000-31508200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:31506000-31508400	Genic enhancers	Spleen	Spleen
19	chr6:31506000-31508600	Transcr. at gene 5' and 3'	Hela-S3	cervix
20	chr6:31506200-31507600	Genic enhancers	Thymus	Thymus
21	chr6:31506200-31507800	Genic enhancers	Colon Smooth Muscle	Colon
22	chr6:31506200-31507800	Genic enhancers	Fetal Intestine Large	intestine
23	chr6:31506200-31508000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
24	chr6:31506200-31508200	Genic enhancers	Small Intestine	intestine
25	chr6:31506200-31508400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
26	chr6:31506200-31508800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:31506200-31509400	Transcr. at gene 5' and 3'	Dnd41	blood
28	chr6:31506400-31507600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:31506400-31507800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:31506400-31507800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:31506400-31507800	Genic enhancers	Fetal Brain Male	brain
32	chr6:31506400-31507800	Genic enhancers	Fetal Muscle Leg	muscle
33	chr6:31506400-31507800	Genic enhancers	Fetal Stomach	stomach
34	chr6:31506400-31507800	Genic enhancers	Pancreas	Pancrea
35	chr6:31506400-31507800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
36	chr6:31506400-31508000	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr6:31506400-31508000	Genic enhancers	Liver	Liver
38	chr6:31506400-31508000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:31506400-31508000	Genic enhancers	Gastric	stomach
40	chr6:31506400-31508000	Genic enhancers	Rectal Mucosa Donor 31	rectum
41	chr6:31506400-31508000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
42	chr6:31506400-31508200	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:31506400-31508200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:31506400-31508200	Genic enhancers	Brain Substantia Nigra	brain
45	chr6:31506400-31508200	Transcr. at gene 5' and 3'	NH-A	brain
46	chr6:31506400-31508400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
47	chr6:31506400-31508400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:31506400-31508400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
49	chr6:31506400-31509000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
50	chr6:31506400-31509000	Transcr. at gene 5' and 3'	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links