Variant report

Variant	rs15297
Chromosome Location	chr6:30709364-30709365
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:0)
Chromatin interactive
region (count:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCB1	chr6:30707405-30712696	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:30709185-30711328	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:30709183-30712741	K562	blood:	n/a	n/a
4	POLR2A	chr6:30704670-30712656	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr6:30708838-30712666	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr6:30708868-30712745	HCT-116	colon:	n/a	n/a
7	ZNF143	chr6:30709335-30711398	Hela-S3	cervix:	n/a	chr6:30710926-30710944
8	POLR2A	chr6:30707434-30712732	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr6:30707893-30713121	HepG2	liver:	n/a	n/a
10	SIN3AK20	chr6:30709089-30712768	HCT-116	colon:	n/a	n/a
11	TCF12	chr6:30709232-30712934	A549	lung:	n/a	chr6:30710631-30710641
12	POLR2A	chr6:30708940-30712572	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:30709207-30712588	HepG2	liver:	n/a	n/a
14	MAX	chr6:30709328-30712883	HCT-116	colon:	n/a	chr6:30710671-30710680
15	CHD1	chr6:30707429-30712681	IMR90	lung:	n/a	chr6:30710901-30710911 chr6:30710526-30710536
16	POLR2A	chr6:30709147-30712541	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:30709207-30712681	HCT-116	colon:	n/a	n/a
18	POLR2A	chr6:30707359-30712662	Hela-S3	cervix:	n/a	n/a
19	TEAD4	chr6:30709194-30712744	K562	blood:	n/a	n/a
20	ELF1	chr6:30709282-30712770	HCT-116	colon:	n/a	n/a
21	POLR2A	chr6:30709151-30712589	GM12891	blood:	n/a	n/a
22	SIN3AK20	chr6:30709235-30709469	A549	lung:	n/a	n/a
23	POLR2A	chr6:30709316-30709372	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:30709185-30712550	GM12891	blood:	n/a	n/a
25	WRNIP1	chr6:30709318-30709505	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:30704619-30712530	IMR90	lung:	n/a	n/a
27	POLR2A	chr6:30708847-30712517	HepG2	liver:	n/a	n/a
28	POLR2A	chr6:30709077-30712499	K562	blood:	n/a	n/a
29	POLR2A	chr6:30708852-30712554	MCF10A-Er-Src	breast:	n/a	n/a
30	SPI1	chr6:30709234-30709440	K562	blood:	n/a	n/a
31	POLR2A	chr6:30708789-30712673	HepG2	liver:	n/a	n/a
32	CTCF	chr6:30709240-30709390	GM12864	blood:	n/a	n/a
33	SIX5	chr6:30709149-30711324	A549	lung:	n/a	n/a
34	POLR2A	chr6:30708787-30712678	K562	blood:	n/a	n/a
35	POLR2A	chr6:30708985-30712615	U87	brain:	n/a	n/a
36	POLR2A	chr6:30707325-30712778	Hela-S3	cervix:	n/a	n/a
37	ELF1	chr6:30708862-30711131	MCF-7	breast:	n/a	n/a
38	POLR2A	chr6:30708886-30712616	PBDE	blood:	n/a	n/a
39	POLR2A	chr6:30709055-30712541	GM12878	blood:	n/a	n/a
40	HCFC1	chr6:30709184-30712726	Hela-S3	cervix:	n/a	n/a
41	HEY1	chr6:30707427-30712781	HepG2	liver:	n/a	chr6:30710563-30710578
42	SP1	chr6:30709172-30712785	HCT-116	colon:	n/a	chr6:30710465-30710476 chr6:30710688-30710697 chr6:30712384-30712395 chr6:30710287-30710301 chr6:30710687-30710699 chr6:30710689-30710698 chr6:30710850-30710857 chr6:30710288-30710297 chr6:30710527-30710536 chr6:30710526-30710538 chr6:30710526-30710538 chr6:30710532-30710539 chr6:30710687-30710699 chr6:30710502-30710513 chr6:30710526-30710537
43	POLR2A	chr6:30707409-30712524	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr6:30707894-30712665	U87	brain:	n/a	n/a
45	POLR2A	chr6:30708696-30712691	GM12892	blood:	n/a	n/a
46	MAZ	chr6:30707288-30712786	IMR90	lung:	n/a	chr6:30710671-30710680
47	POLR2A	chr6:30707388-30712490	A549	lung:	n/a	n/a
48	POLR2A	chr6:30708948-30712615	U87	brain:	n/a	n/a
49	POLR2A	chr6:30707270-30712612	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:30709220-30711022	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:30523845..30525398-chr6:30708449..30710069,2	MCF-7	breast:
2	chr6:30707945..30712505-chr6:30840794..30847673,9	K562	blood:
3	chr6:30707658..30710015-chr8:144677120..144679649,2	MCF-7	breast:
4	chr1:117451768..117453895-chr6:30707960..30710700,2	MCF-7	breast:
5	chr6:30581322..30587794-chr6:30705649..30714068,32	K562	blood:
6	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
7	chr6:30639079..30642784-chr6:30705636..30712325,12	MCF-7	breast:
8	chr3:170587537..170588121-chr6:30709146..30709960,2	Hela-S3	cervix:
9	chr5:179050328..179050981-chr6:30708892..30709826,2	Hela-S3	cervix:
10	chr6:30707481..30713943-chr6:30872979..30880006,10	MCF-7	breast:
11	chr6:30614009..30615526-chr6:30709280..30711034,2	MCF-7	breast:
12	chr11:118788904..118790575-chr6:30707843..30710033,2	MCF-7	breast:
13	chr6:30578948..30585851-chr6:30707403..30713755,14	MCF-7	breast:
14	chr6:30705171..30717521-chr6:30843972..30856100,74	MCF-7	breast:
15	chr1:145381364..145383003-chr6:30708944..30710900,2	MCF-7	breast:
16	chr2:64880444..64881386-chr6:30708982..30709803,2	Hela-S3	cervix:
17	chr6:30580645..30587403-chr6:30708153..30714600,16	MCF-7	breast:
18	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
19	chr11:62495454..62497939-chr6:30709047..30710768,2	MCF-7	breast:
20	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
21	chr17:57918223..57923763-chr6:30707801..30713436,10	MCF-7	breast:
22	chr6:30594160..30596394-chr6:30709286..30711112,2	MCF-7	breast:
23	chr6:30537121..30539529-chr6:30708411..30710426,2	MCF-7	breast:
24	chr6:30708700..30710764-chr6:30734085..30735975,2	K562	blood:
25	chr15:60687645..60690491-chr6:30708468..30710482,2	MCF-7	breast:
26	chr17:57922134..57925818-chr6:30708673..30712845,6	MCF-7	breast:
27	chr6:30709068..30709954-chr7:100026485..100027413,2	Hela-S3	cervix:
28	chr6:30707880..30713865-chr6:30880456..30883497,7	MCF-7	breast:
29	chr15:65596039..65597563-chr6:30709238..30711608,2	MCF-7	breast:
30	chr14:81685583..81687779-chr6:30708570..30711390,2	MCF-7	breast:
31	chr6:30651552..30657864-chr6:30708721..30713716,15	MCF-7	breast:

No data

Variant related genes	Relation type
FLOT1	TF binding region
ENSG00000272273	TF binding region
ENSG00000200156	Chromatin interaction
ENSG00000104529	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000186174	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000165417	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000272715	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000264731	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000134247	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000163584	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000179833	Chromatin interaction
ENSG00000182718	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1049943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1136719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264352	0.83[ASN][1000 genomes]
rs17189329	0.85[ASN][1000 genomes]
rs17195712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094128	0.97[ASN][1000 genomes]
rs3130662	1.00[ASN][1000 genomes]
rs3909184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58638768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv970736	chr6:30692055-30710740	Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
10	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv884102	chr6:30706013-30720567	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30690000-30709600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30705400-30709400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:30705400-30709600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:30705800-30709400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
5	chr6:30707000-30709400	Genic enhancers	Placenta	Placenta
6	chr6:30707400-30709400	Genic enhancers	Pancreas	Pancrea
7	chr6:30707800-30709400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:30707800-30709400	Genic enhancers	Lung	lung
9	chr6:30707800-30709400	Genic enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:30707800-30709600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:30707800-30709600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:30708000-30709400	Genic enhancers	Spleen	Spleen
13	chr6:30708000-30709400	Transcr. at gene 5' and 3'	NHLF	lung
14	chr6:30708200-30709400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr6:30708200-30709400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:30708200-30709400	Genic enhancers	Fetal Thymus	thymus
17	chr6:30708400-30709400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:30708400-30709400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:30708400-30709400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:30708400-30709400	Weak transcription	Aorta	Aorta
21	chr6:30708400-30709600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:30708600-30709400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:30708600-30709400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:30708600-30709400	Weak transcription	HMEC	breast
25	chr6:30708800-30709400	Genic enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:30708800-30709400	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:30708800-30709400	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr6:30708800-30709400	Genic enhancers	Fetal Muscle Leg	muscle
29	chr6:30708800-30709400	Enhancers	Ovary	ovary
30	chr6:30708800-30710000	Flanking Active TSS	Hela-S3	cervix
31	chr6:30708800-30710200	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr6:30708800-30710200	Flanking Active TSS	Dnd41	blood
33	chr6:30708800-30710400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
34	chr6:30709000-30709400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:30709000-30709400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:30709000-30709400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:30709000-30709400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
38	chr6:30709000-30709400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:30709000-30709400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:30709000-30709400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
41	chr6:30709000-30709400	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
42	chr6:30709000-30709400	Genic enhancers	Esophagus	oesophagus
43	chr6:30709000-30709400	Genic enhancers	Fetal Intestine Large	intestine
44	chr6:30709000-30709400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
45	chr6:30709000-30709400	Transcr. at gene 5' and 3'	HepG2	liver
46	chr6:30709000-30709600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:30709000-30709600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:30709000-30709600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
49	chr6:30709000-30709600	Enhancers	Small Intestine	intestine
50	chr6:30709000-30709600	Transcr. at gene 5' and 3'	A549	lung

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