Variant report

Variant	rs4252605
Chromosome Location	chr17:37862177-37862178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:67)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:67 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr17:37862046-37862284	MCF10A-Er-Src	breast:	n/a	n/a
2	NFIC	chr17:37861848-37862854	ECC-1	luminal epithelium:	n/a	n/a
3	GATA3	chr17:37861887-37862639	MCF-7	breast:	n/a	n/a
4	CTCF	chr17:37862060-37862210	SAEC	small airway:	n/a	n/a
5	ESR1	chr17:37861926-37862532	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr17:37861870-37862736	T-47D	breast:	n/a	n/a
7	GATA3	chr17:37862025-37862515	MCF-7	breast:	n/a	n/a
8	JUND	chr17:37861976-37862522	MCF-7	breast:	n/a	n/a
9	TEAD4	chr17:37861820-37862711	ECC-1	luminal epithelium:	n/a	n/a
10	RAD21	chr17:37861858-37862642	ECC-1	luminal epithelium:	n/a	chr17:37861927-37861936 chr17:37862153-37862165
11	EP300	chr17:37861903-37862549	ECC-1	luminal epithelium:	n/a	n/a
12	SIN3AK20	chr17:37861887-37862558	MCF-7	breast:	n/a	n/a
13	CTCF	chr17:37862080-37862230	SAEC	small airway:	n/a	n/a
14	JUND	chr17:37861888-37862628	MCF-7	breast:	n/a	n/a
15	STAT3	chr17:37862031-37862231	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr17:37862049-37862334	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr17:37861917-37862428	MCF-7	breast:	n/a	n/a
18	ESR1	chr17:37861965-37862476	ECC-1	luminal epithelium:	n/a	n/a
19	FOS	chr17:37862069-37862322	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr17:37862047-37862291	MCF10A-Er-Src	breast:	n/a	n/a
21	HDAC2	chr17:37861930-37862513	MCF-7	breast:	n/a	n/a
22	FOSL2	chr17:37861922-37862587	MCF-7	breast:	n/a	n/a
23	NR2F2	chr17:37861927-37862659	MCF-7	breast:	n/a	n/a
24	FOXM1	chr17:37861892-37862628	ECC-1	luminal epithelium:	n/a	n/a
25	SP1	chr17:37861803-37862660	HCT-116	colon:	n/a	chr17:37862159-37862173
26	MAX	chr17:37861887-37862723	ECC-1	luminal epithelium:	n/a	n/a
27	EP300	chr17:37861795-37862717	ECC-1	luminal epithelium:	n/a	n/a
28	STAT3	chr17:37862044-37862284	MCF10A-Er-Src	breast:	n/a	n/a
29	GATA3	chr17:37861931-37862616	T-47D	breast:	n/a	n/a
30	ZBTB7A	chr17:37861365-37862697	ECC-1	luminal epithelium:	n/a	n/a
31	GATA3	chr17:37861933-37862620	T-47D	breast:	n/a	n/a
32	STAT3	chr17:37862041-37862224	MCF10A-Er-Src	breast:	n/a	n/a
33	ZNF217	chr17:37862076-37862619	MCF-7	breast:	n/a	n/a
34	HDAC2	chr17:37861872-37862531	MCF-7	breast:	n/a	n/a
35	ESR1	chr17:37861945-37862516	ECC-1	luminal epithelium:	n/a	n/a
36	TCF12	chr17:37861765-37862864	ECC-1	luminal epithelium:	n/a	chr17:37862493-37862500 chr17:37862385-37862392
37	FOXM1	chr17:37861810-37862548	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr17:37861941-37862344	HCT-116	colon:	n/a	n/a
39	POLR2A	chr17:37861897-37862559	ECC-1	luminal epithelium:	n/a	n/a
40	FOXA1	chr17:37861971-37862611	T-47D	breast:	n/a	n/a
41	SIN3AK20	chr17:37861774-37862777	MCF-7	breast:	n/a	n/a
42	ZBTB7A	chr17:37861886-37862638	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr17:37862042-37862285	HCT-116	colon:	n/a	n/a
44	NFIC	chr17:37861801-37862796	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr17:37861870-37862621	ECC-1	luminal epithelium:	n/a	n/a
46	MYC	chr17:37862087-37862218	MCF-7	breast:	n/a	n/a
47	GATA3	chr17:37861741-37862791	MCF-7	breast:	n/a	chr17:37861831-37861843 chr17:37861833-37861840 chr17:37861833-37861842 chr17:37861830-37861840 chr17:37861829-37861845 chr17:37861832-37861842 chr17:37861834-37861851
48	CTCF	chr17:37862120-37862270	HMEC	breast:	n/a	n/a
49	ESR1	chr17:37861985-37862372	T-47D	breast:	n/a	n/a
50	USF1	chr17:37861966-37862551	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:37861008..37863729-chr17:37884662..37888113,4	MCF-7	breast:
2	chr17:37859950..37863403-chr17:37895808..37898808,3	MCF-7	breast:
3	chr17:37861753..37864572-chr17:37866139..37867731,2	MCF-7	breast:
4	chr17:37860742..37863626-chr17:37884816..37888176,3	MCF-7	breast:
5	chr17:37860215..37862693-chr17:37863560..37866176,3	K562	blood:
6	chr17:37858020..37860192-chr17:37861876..37864299,2	K562	blood:
7	chr17:37855173..37857494-chr17:37859476..37862807,3	K562	blood:
8	chr17:37854371..37858847-chr17:37859204..37863861,12	MCF-7	breast:
9	chr17:37860257..37864274-chr17:37871854..37875164,5	MCF-7	breast:
10	chr17:37842383..37849519-chr17:37854521..37862509,17	MCF-7	breast:
11	chr17:37860636..37865251-chr17:37890921..37895460,5	MCF-7	breast:

No data

Variant related genes	Relation type
ERBB2	TF binding region
ENSG00000161395	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000141736	Chromatin interaction
ENSG00000141741	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12936456	1.00[AMR][1000 genomes]
rs12943460	1.00[AMR][1000 genomes]
rs12950412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12951747	1.00[AFR][1000 genomes]
rs34715089	0.80[AFR][1000 genomes]
rs35527921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35938081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4252625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4252630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs66788250	0.80[AFR][1000 genomes]
rs71369787	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	20 gene(s)	inside rSNPs	diseases
6	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37857000-37872000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:37857600-37863400	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr17:37857800-37863200	Enhancers	Left Ventricle	heart
4	chr17:37858000-37862200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:37858000-37862400	Genic enhancers	Fetal Stomach	stomach
6	chr17:37858000-37862800	Genic enhancers	Fetal Intestine Large	intestine
7	chr17:37858000-37863200	Weak transcription	HUVEC	blood vessel
8	chr17:37858000-37885200	Weak transcription	Fetal Brain Male	brain
9	chr17:37858000-37885600	Weak transcription	Hela-S3	cervix
10	chr17:37858200-37862200	Enhancers	Lung	lung
11	chr17:37858200-37862400	Enhancers	Fetal Lung	lung
12	chr17:37858200-37862400	Enhancers	Gastric	stomach
13	chr17:37858200-37862400	Enhancers	Pancreas	Pancrea
14	chr17:37858200-37863200	Weak transcription	Spleen	Spleen
15	chr17:37858200-37863200	Weak transcription	NHLF	lung
16	chr17:37858200-37863600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:37858200-37864000	Enhancers	Liver	Liver
18	chr17:37858200-37864400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:37858200-37882600	Weak transcription	NHDF-Ad	bronchial
20	chr17:37858400-37862400	Enhancers	Duodenum Mucosa	Duodenum
21	chr17:37858400-37863000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr17:37858400-37863400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr17:37858400-37863400	Weak transcription	Fetal Kidney	kidney
24	chr17:37858400-37863600	Genic enhancers	Fetal Intestine Small	intestine
25	chr17:37858400-37879600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr17:37858800-37862200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr17:37858800-37862800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr17:37859000-37863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:37859000-37864000	Genic enhancers	Fetal Muscle Leg	muscle
30	chr17:37859200-37862200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr17:37859200-37863000	Enhancers	Right Ventricle	heart
32	chr17:37859400-37881000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:37859600-37863600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:37859800-37862200	Enhancers	Placenta	Placenta
35	chr17:37859800-37864800	Weak transcription	Fetal Brain Female	brain
36	chr17:37860200-37862200	Enhancers	HepG2	liver
37	chr17:37860200-37862800	Enhancers	Stomach Smooth Muscle	stomach
38	chr17:37860200-37863000	Enhancers	Stomach Mucosa	stomach
39	chr17:37860400-37862400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr17:37860400-37862600	Enhancers	A549	lung
41	chr17:37860600-37862200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr17:37860600-37862600	Enhancers	HSMMtube	muscle
43	chr17:37860800-37862800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr17:37860800-37862800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr17:37860800-37862800	Enhancers	Aorta	Aorta
46	chr17:37861000-37862200	Enhancers	HMEC	breast
47	chr17:37861000-37862400	Enhancers	Right Atrium	heart
48	chr17:37861000-37862800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr17:37861000-37862800	Enhancers	NH-A	brain
50	chr17:37861000-37863000	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links