Variant report

Variant	rs559785439
Chromosome Location	chr6:27775468-27775469
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:265)
CpG islands
(count:0)
Chromatin interactive
region (count:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:265 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27774540-27777234	PANC-1	pancreas:	n/a	n/a
2	ELF1	chr6:27774770-27775784	K562	blood:	n/a	n/a
3	ETS1	chr6:27775247-27776094	K562	blood:	n/a	n/a
4	FOSL2	chr6:27775283-27776333	HepG2	liver:	n/a	chr6:27775775-27775784
5	POLR2A	chr6:27774760-27777233	Hela-S3	cervix:	n/a	n/a
6	TAF7	chr6:27774212-27776082	H1-hESC	embryonic stem cell:	n/a	n/a
7	POU2F2	chr6:27774658-27776961	GM12878	blood:	n/a	n/a
8	SIN3AK20	chr6:27775223-27776438	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:27774575-27779531	GM12891	blood:	n/a	n/a
10	TCF12	chr6:27775190-27776321	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:27774742-27776963	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:27774756-27777061	SK-N-SH	brain:	n/a	n/a
13	REST	chr6:27775196-27775767	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr6:27774692-27777073	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:27774769-27775764	A549	lung:	n/a	n/a
16	POLR2A	chr6:27774397-27776944	K562	blood:	n/a	n/a
17	MYC	chr6:27774708-27776113	NB4	blood:	n/a	n/a
18	NR2F2	chr6:27774632-27775477	K562	blood:	n/a	n/a
19	POLR2A	chr6:27775218-27776944	U87	brain:	n/a	n/a
20	POLR2A	chr6:27773932-27776060	K562	blood:	n/a	n/a
21	POLR2A	chr6:27774750-27776914	Raji	blood:	n/a	n/a
22	POLR2A	chr6:27774382-27779662	K562	blood:	n/a	n/a
23	MAX	chr6:27774721-27775508	K562	blood:	n/a	n/a
24	HA-E2F1	chr6:27774879-27776430	MCF-7	breast:	n/a	chr6:27775901-27775912 chr6:27775901-27775908 chr6:27775901-27775908 chr6:27775896-27775911 chr6:27775901-27775908 chr6:27775900-27775909
25	POLR2A	chr6:27774757-27777348	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr6:27774349-27776475	MCF-7	breast:	n/a	n/a
27	BCLAF1	chr6:27774813-27775532	GM12878	blood:	n/a	n/a
28	USF1	chr6:27775245-27775674	HepG2	liver:	n/a	n/a
29	JUND	chr6:27775307-27776476	A549	lung:	n/a	chr6:27775775-27775784
30	POLR2A	chr6:27774870-27776987	HepG2	liver:	n/a	n/a
31	MYBL2	chr6:27774663-27777031	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:27774642-27777227	GM12892	blood:	n/a	n/a
33	POLR2A	chr6:27774553-27777195	GM15510	blood:	n/a	n/a
34	USF2	chr6:27774834-27775546	K562	blood:	n/a	n/a
35	POLR2A	chr6:27774376-27777210	GM12892	blood:	n/a	n/a
36	HEY1	chr6:27774566-27777492	HepG2	liver:	n/a	n/a
37	IRF4	chr6:27775226-27775806	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:27775251-27775706	A549	lung:	n/a	n/a
39	MAX	chr6:27774838-27775638	A549	lung:	n/a	n/a
40	PAX5	chr6:27774758-27775695	GM12878	blood:	n/a	n/a
41	SP1	chr6:27775290-27776735	A549	lung:	n/a	n/a
42	MYC	chr6:27774835-27776024	K562	blood:	n/a	n/a
43	EP300	chr6:27774639-27776110	A549	lung:	n/a	n/a
44	ZBTB33	chr6:27775260-27775750	K562	blood:	n/a	n/a
45	PAX5	chr6:27775419-27775680	GM12878	blood:	n/a	n/a
46	SP1	chr6:27775385-27776101	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr6:27774441-27779690	PBDE	blood:	n/a	n/a
48	SP1	chr6:27775315-27776431	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:27774262-27776064	K562	blood:	n/a	n/a
50	ZBTB33	chr6:27775396-27776077	SK-N-SH	brain:	n/a	n/a

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:69978747..69979546-chr6:27775291..27775940,2	NB4	blood:
2	chr6:26203418..26208290-chr6:27773529..27778557,7	MCF-7	breast:
3	chr6:26055768..26057563-chr6:27773736..27776348,2	MCF-7	breast:
4	chr6:27620343..27622323-chr6:27775251..27777000,2	K562	blood:
5	chr6:27356362..27358956-chr6:27773296..27775539,3	K562	blood:
6	chr6:26183066..26187877-chr6:27774821..27779151,5	MCF-7	breast:
7	chr6:27112242..27117659-chr6:27770082..27780470,17	MCF-7	breast:
8	chr6:27093369..27111594-chr6:27770152..27782376,64	K562	blood:
9	chr6:26025755..26029009-chr6:27774713..27777489,4	MCF-7	breast:
10	chr6:26029311..26033760-chr6:27774369..27777821,5	MCF-7	breast:
11	chr6:26282374..26290542-chr6:27772727..27779446,9	MCF-7	breast:
12	chr12:122238688..122240991-chr6:27775066..27777926,2	MCF-7	breast:
13	chr6:27098259..27104331-chr6:27773668..27779939,16	MCF-7	breast:
14	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
15	chr4:74123460..74124971-chr6:27773658..27776230,2	MCF-7	breast:
16	chr6:26124249..26127079-chr6:27774998..27777814,2	MCF-7	breast:
17	chr6:26270357..26275628-chr6:27773210..27778290,5	MCF-7	breast:
18	chr6:26196862..26203126-chr6:27774221..27779033,8	MCF-7	breast:
19	chr6:27217680..27220381-chr6:27773874..27775997,2	K562	blood:
20	chr6:27094403..27106138-chr6:27772392..27783072,46	MCF-7	breast:
21	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
22	chr20:46253914..46256235-chr6:27775135..27778059,2	MCF-7	breast:
23	chr6:26216294..26218815-chr6:27772946..27775743,3	MCF-7	breast:
24	chr6:26201617..26205446-chr6:27775076..27778001,4	K562	blood:
25	chr6:26158302..26159117-chr6:27775211..27776028,3	Hela-S3	cervix:
26	chr11:62608524..62609452-chr6:27775275..27775944,3	NB4	blood:
27	chr6:27774293..27778194-chr6:28301096..28304976,3	K562	blood:
28	chr6:26204792..26206368-chr6:27774871..27776678,2	MCF-7	breast:
29	chr6:27775362..27779371-chr6:28186093..28189957,4	K562	blood:
30	chr6:27111749..27120986-chr6:27774460..27781468,38	K562	blood:
31	chr6:26197916..26207803-chr6:27772547..27779655,13	K562	blood:

No data

Variant related genes	Relation type
HIST1H3H	TF binding region
HIST1H2AI	TF binding region
ENSG00000139725	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000217275	Chromatin interaction
ENSG00000218690	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000168242	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000216676	Chromatin interaction
ENSG00000250220	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000166226	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000132466	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000197697	Chromatin interaction
ENSG00000184825	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
8	nsv969366	chr6:27775188-27776471	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	57 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27774200-27778000	Active TSS	K562	blood
2	chr6:27774200-27779200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:27774200-27779200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:27774200-27779400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:27774200-27779800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:27774200-27779800	Active TSS	Thymus	Thymus
7	chr6:27774200-27779800	Active TSS	A549	lung
8	chr6:27774400-27775600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr6:27774400-27775600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:27774400-27775600	Flanking Active TSS	Fetal Muscle Trunk	muscle
11	chr6:27774400-27776200	Active TSS	Rectal Smooth Muscle	rectum
12	chr6:27774400-27776400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:27774400-27776400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
14	chr6:27774400-27776400	Active TSS	Fetal Kidney	kidney
15	chr6:27774400-27776400	Active TSS	Fetal Lung	lung
16	chr6:27774400-27776400	Active TSS	NHLF	lung
17	chr6:27774400-27776800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:27774400-27776800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:27774400-27777000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:27774400-27777200	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr6:27774400-27778400	Active TSS	Brain Germinal Matrix	brain
22	chr6:27774400-27778400	Active TSS	Fetal Intestine Large	intestine
23	chr6:27774400-27778800	Active TSS	Fetal Brain Female	brain
24	chr6:27774400-27779000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:27774400-27779200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:27774400-27779200	Active TSS	NHDF-Ad	bronchial
27	chr6:27774400-27780000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr6:27774400-27780000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:27774400-27780000	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr6:27774400-27780000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:27774400-27780200	Active TSS	H1 Cell Line	embryonic stem cell
32	chr6:27774400-27784000	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr6:27774600-27775600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr6:27774600-27775600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr6:27774600-27775600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:27774600-27775800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr6:27774600-27776400	Active TSS	Aorta	Aorta
38	chr6:27774600-27776400	Active TSS	HSMM	muscle
39	chr6:27774600-27776600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr6:27774600-27779600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:27774800-27775600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr6:27774800-27775600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr6:27774800-27775600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:27774800-27775600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
45	chr6:27774800-27775800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
46	chr6:27774800-27776200	Active TSS	Ovary	ovary
47	chr6:27774800-27776400	Active TSS	Fetal Heart	heart
48	chr6:27774800-27776600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
49	chr6:27774800-27776600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:27774800-27776600	Active TSS	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links