Variant report

Variant	rs10085718
Chromosome Location	chr7:7606194-7606195
allele	C/T
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	STAT3	chr7:7606076-7606269	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:7606188-7606864	HUVEC	blood vessel:	n/a	n/a
3	GTF2F1	chr7:7606009-7606570	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr7:7605323-7606257	MCF-7	breast:	n/a	n/a
5	POLR2A	chr7:7606070-7606975	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr7:7606098-7606643	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:7606180-7607287	GM15510	blood:	n/a	n/a
8	POLR2A	chr7:7606007-7607182	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr7:7606180-7609855	GM12892	blood:	n/a	n/a
10	FOXM1	chr7:7606182-7606802	GM12878	blood:	n/a	n/a
11	RELA	chr7:7606037-7606741	GM19193	blood:	n/a	n/a
12	TCF12	chr7:7606087-7607097	ECC-1	luminal epithelium:	n/a	n/a
13	YY1	chr7:7606089-7607374	SK-N-SH	brain:	n/a	chr7:7606745-7606754 chr7:7606431-7606445 chr7:7606746-7606760 chr7:7606613-7606623 chr7:7606880-7606891 chr7:7606613-7606635 chr7:7606745-7606756 chr7:7606642-7606656 chr7:7606614-7606622 chr7:7606616-7606624 chr7:7606611-7606630 chr7:7606642-7606653
14	SMARCC1	chr7:7605797-7607113	Hela-S3	cervix:	n/a	n/a
15	RFX5	chr7:7606171-7606460	HepG2	liver:	n/a	n/a
16	FOS	chr7:7606173-7606237	MCF10A-Er-Src	breast:	n/a	n/a
17	IRF1	chr7:7606191-7606751	K562	blood:	n/a	chr7:7606433-7606447 chr7:7606487-7606501
18	MAX	chr7:7606159-7607702	NB4	blood:	n/a	n/a
19	MAX	chr7:7606182-7607561	SK-N-SH	brain:	n/a	n/a
20	MAX	chr7:7606186-7607482	Hela-S3	cervix:	n/a	n/a
21	GATA3	chr7:7605456-7606748	T-47D	breast:	n/a	n/a
22	POLR2A	chr7:7606181-7606930	HCT-116	colon:	n/a	n/a
23	FOXA1	chr7:7606031-7606392	HepG2	liver:	n/a	n/a
24	POLR2A	chr7:7606189-7607219	PANC-1	pancreas:	n/a	n/a
25	RXRA	chr7:7606146-7606755	HepG2	liver:	n/a	n/a
26	EP300	chr7:7606166-7606750	GM12878	blood:	n/a	chr7:7606636-7606652 chr7:7606681-7606690
27	RELA	chr7:7606193-7606912	GM19099	blood:	n/a	n/a
28	GABPA	chr7:7606141-7606906	A549	lung:	n/a	chr7:7606645-7606654
29	GABPA	chr7:7606146-7606886	K562	blood:	n/a	chr7:7606645-7606654
30	HA-E2F1	chr7:7605009-7607192	MCF-7	breast:	n/a	chr7:7606877-7606887 chr7:7606645-7606654
31	POLR2A	chr7:7606157-7606907	U87	brain:	n/a	n/a
32	POLR2A	chr7:7606116-7606948	SK-N-SH	brain:	n/a	n/a
33	FOXA2	chr7:7606013-7606292	HepG2	liver:	n/a	n/a
34	FOS	chr7:7606056-7606351	MCF10A-Er-Src	breast:	n/a	n/a
35	CHD2	chr7:7606108-7607149	GM12878	blood:	n/a	n/a
36	SP1	chr7:7606132-7606751	A549	lung:	n/a	chr7:7606433-7606445 chr7:7606487-7606499 chr7:7606458-7606467 chr7:7606458-7606468 chr7:7606651-7606660 chr7:7606644-7606656 chr7:7606459-7606468 chr7:7606644-7606656 chr7:7606646-7606655 chr7:7606430-7606444 chr7:7606484-7606498 chr7:7606489-7606498 chr7:7606457-7606469 chr7:7606487-7606499 chr7:7606458-7606467 chr7:7606457-7606469
37	RUNX3	chr7:7606189-7607351	GM12878	blood:	n/a	n/a
38	POLR2A	chr7:7606175-7606850	SK-N-MC	brain:	n/a	n/a
39	TAF1	chr7:7606037-7606891	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr7:7606014-7607284	GM18951	blood:	n/a	n/a
41	BHLHE40	chr7:7606082-7606889	GM12878	blood:	n/a	chr7:7606640-7606656 chr7:7606873-7606889
42	JUND	chr7:7606094-7606257	HepG2	liver:	n/a	chr7:7606199-7606210
43	YY1	chr7:7606185-7607053	SK-N-SH_RA	brain:	n/a	chr7:7606745-7606754 chr7:7606431-7606445 chr7:7606746-7606760 chr7:7606613-7606623 chr7:7606880-7606891 chr7:7606613-7606635 chr7:7606745-7606756 chr7:7606642-7606656 chr7:7606614-7606622 chr7:7606616-7606624 chr7:7606611-7606630 chr7:7606642-7606653
44	FOXA1	chr7:7605585-7606643	T-47D	breast:	n/a	n/a
45	TEAD4	chr7:7605853-7606394	HepG2	liver:	n/a	n/a
46	RCOR1	chr7:7605950-7606744	GM12878	blood:	n/a	n/a
47	HDAC2	chr7:7605478-7606881	MCF-7	breast:	n/a	chr7:7606261-7606275
48	SIN3AK20	chr7:7605360-7607539	MCF-7	breast:	n/a	n/a
49	CHD1	chr7:7606065-7606432	H1-hESC	embryonic stem cell:	n/a	n/a
50	CHD2	chr7:7606185-7607072	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7605830..7608267-chr7:7679102..7681869,5	MCF-7	breast:
2	chr19:38863925..38865445-chr7:7605772..7607416,2	MCF-7	breast:
3	chr7:7603096..7605323-chr7:7605419..7606942,2	MCF-7	breast:
4	chr7:7604819..7606875-chr7:8300807..8302647,2	MCF-7	breast:
5	chr7:7588099..7594648-chr7:7604621..7611487,9	MCF-7	breast:
6	chr7:7605040..7608458-chr7:7677009..7681661,8	K562	blood:
7	chr7:7588174..7592470-chr7:7605427..7608009,3	MCF-7	breast:
8	chr7:7221023..7222531-chr7:7605504..7608100,2	MCF-7	breast:
9	chr7:7605958..7609334-chr7:7621457..7626452,6	MCF-7	breast:
10	chr7:7220051..7223731-chr7:7605300..7608795,5	K562	blood:
11	chr7:7602250..7604116-chr7:7605056..7607098,3	K562	blood:
12	chr7:7603046..7608569-chr7:7677123..7682101,8	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL28A1-1	chr7:7605545-7606237	XLOC_006350
2	lnc-COL28A1-1	chr7:7605545-7606627	ENSG00000272894.1

Variant related genes	Relation type
MIOS	TF binding region
ENSG00000272894	TF binding region
ENSG00000164654	Chromatin interaction
ENSG00000229970	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000106392	Chromatin interaction
ENSG00000272894	Chromatin interaction
ENSG00000003147	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000244239	Chromatin interaction
ENSG00000219545	Chromatin interaction
ENSG00000272732	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12535954	1.00[ASN][1000 genomes]
rs17167617	1.00[ASN][1000 genomes]
rs2348047	1.00[ASN][1000 genomes]
rs28847278	1.00[ASN][1000 genomes]
rs6463702	1.00[ASN][1000 genomes]
rs6962939	1.00[ASN][1000 genomes]
rs73346346	1.00[ASN][1000 genomes]
rs73347196	1.00[ASN][1000 genomes]
rs73347201	1.00[ASN][1000 genomes]
rs73348905	1.00[ASN][1000 genomes]
rs7801367	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	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7590000-7606200	Weak transcription	Ovary	ovary
2	chr7:7597200-7606600	Weak transcription	Gastric	stomach
3	chr7:7602800-7606400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:7603600-7606200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:7603600-7606400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr7:7604200-7606200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr7:7604200-7607800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:7604400-7606200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr7:7605200-7606400	Flanking Active TSS	NHEK	skin
10	chr7:7605200-7607400	Active TSS	Pancreas	Pancrea
11	chr7:7605400-7606200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:7605400-7606200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:7605400-7606200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr7:7605400-7607400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr7:7605600-7606200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr7:7605600-7606400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:7605600-7606400	Flanking Active TSS	Dnd41	blood
18	chr7:7605600-7607400	Active TSS	Fetal Kidney	kidney
19	chr7:7605600-7607400	Active TSS	Rectal Smooth Muscle	rectum
20	chr7:7605800-7606200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
21	chr7:7605800-7606200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
22	chr7:7605800-7606200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:7605800-7606200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr7:7605800-7606200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr7:7605800-7606200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:7605800-7606200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr7:7605800-7606200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr7:7605800-7606200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr7:7605800-7606200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:7605800-7606200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:7605800-7606200	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr7:7605800-7606200	Flanking Active TSS	Colonic Mucosa	Colon
33	chr7:7605800-7606200	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr7:7605800-7606200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr7:7605800-7606200	Flanking Active TSS	Fetal Intestine Large	intestine
36	chr7:7605800-7606200	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr7:7605800-7606200	Flanking Active TSS	Placenta	Placenta
38	chr7:7605800-7606200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr7:7605800-7606200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr7:7605800-7606200	Flanking Active TSS	Stomach Mucosa	stomach
41	chr7:7605800-7606200	Flanking Active TSS	GM12878-XiMat	blood
42	chr7:7605800-7606200	Flanking Active TSS	Hela-S3	cervix
43	chr7:7605800-7606200	Flanking Active TSS	HepG2	liver
44	chr7:7605800-7606200	Enhancers	Osteobl	bone
45	chr7:7605800-7606400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr7:7605800-7606400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr7:7605800-7606400	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr7:7605800-7606400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:7605800-7606400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr7:7605800-7606400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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