Variant report

Variant	rs11653988
Chromosome Location	chr17:18088833-18088834
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	CHD1	chr17:18085856-18091134	IMR90	lung:	n/a	n/a
2	CTCF	chr17:18088800-18088950	SK-N-SH_RA	brain:	n/a	n/a
3	MXI1	chr17:18085581-18092228	SK-N-SH	brain:	n/a	chr17:18086672-18086687 chr17:18088362-18088377
4	SIN3AK20	chr17:18088750-18089006	PFSK-1	brain:	n/a	n/a
5	CTCF	chr17:18088780-18088930	NHDF-neo	bronchial:	n/a	n/a
6	CTCF	chr17:18088760-18088910	HPAF	blood vessel:	n/a	n/a
7	CTCF	chr17:18088806-18088886	HUVEC	blood vessel:	n/a	n/a
8	BRCA1	chr17:18087921-18089168	Hela-S3	cervix:	n/a	chr17:18088984-18088991
9	POLR2A	chr17:18088811-18089707	U87	brain:	n/a	n/a
10	MAZ	chr17:18085721-18089121	IMR90	lung:	n/a	chr17:18086307-18086316 chr17:18086746-18086755 chr17:18087462-18087472
11	EP300	chr17:18087589-18092262	SK-N-SH	brain:	n/a	chr17:18089998-18090012
12	WRNIP1	chr17:18087774-18091201	GM12878	blood:	n/a	n/a
13	HCFC1	chr17:18085487-18088855	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr17:18088740-18088890	HRPEpiC	eye:	n/a	n/a
15	MYC	chr17:18088495-18090406	MCF10A-Er-Src	breast:	n/a	chr17:18089982-18089991
16	KAP1	chr17:18087725-18091513	HEK293	kidney:	n/a	chr17:18091056-18091064
17	CTCF	chr17:18088805-18088875	LNCaP	prostate:	n/a	n/a
18	RAD21	chr17:18088739-18088931	SK-N-SH_RA	brain:	n/a	n/a
19	CTCF	chr17:18088780-18088930	AG10803	skin:	n/a	n/a
20	EBF1	chr17:18088782-18089554	GM12878	blood:	n/a	chr17:18088851-18088860 chr17:18089374-18089385
21	SIN3A	chr17:18085887-18089147	H1-hESC	embryonic stem cell:	n/a	chr17:18086499-18086508 chr17:18086322-18086336
22	CTCF	chr17:18088740-18088890	AG04450	lung:	n/a	n/a
23	POLR2A	chr17:18085568-18089598	IMR90	lung:	n/a	n/a
24	CTCF	chr17:18088700-18088850	HCPEpiC	choroid plexus:	n/a	n/a
25	CTCF	chr17:18088740-18088890	AG09319	gingival:	n/a	n/a
26	MXI1	chr17:18086003-18091020	IMR90	lung:	n/a	chr17:18086672-18086687 chr17:18088362-18088377
27	POLR2A	chr17:18088811-18089126	U87	brain:	n/a	n/a
28	CTCF	chr17:18088820-18088970	AG04449	skin:	n/a	n/a
29	RAD21	chr17:18088641-18089002	SK-N-SH_RA	brain:	n/a	n/a
30	CHD1	chr17:18086161-18089744	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18057503..18062681-chr17:18084968..18089396,8	MCF-7	breast:
2	chr17:18085197..18089449-chr17:18160313..18164902,6	K562	blood:
3	chr17:18059406..18063498-chr17:18086302..18089651,4	K562	blood:
4	chr17:18061742..18067292-chr17:18083221..18089651,7	K562	blood:
5	chr17:18088345..18089995-chr17:18161627..18163535,2	K562	blood:
6	chr17:18088174..18090098-chr17:18107695..18110027,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FLII-3	chr17:18088550-18088914	predAs_chen_AI570526_1

Variant related genes	Relation type
ENSG00000266677	TF binding region
ENSG00000177731	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000091536	Chromatin interaction
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10048161	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451244	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078412	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652964	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11654146	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654177	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654741	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655588	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655731	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11655797	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656035	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11657194	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11658477	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11868832	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868886	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11871039	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11871491	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600694	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563371	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563373	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16960980	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960983	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960986	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960990	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960996	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015336	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28811342	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088233	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34474249	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36058389	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55918833	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58441148	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59354912	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60285171	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072464	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62072465	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072466	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072467	0.90[EUR][1000 genomes]
rs62072468	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072496	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62072497	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62072498	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072500	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073602	0.90[EUR][1000 genomes]
rs62073603	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62073604	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62073605	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62073606	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62073607	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073608	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073609	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073611	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62073615	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62073649	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073650	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502640	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207276	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs735960	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8065026	0.90[EUR][1000 genomes]
rs8069094	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077577	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9916193	0.90[EUR][1000 genomes]
rs997315	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription 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 miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv3411665	chr17:18085527-18089325	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	esv3376987	chr17:18086452-18089000	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 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	chr17:18085600-18089000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:18085600-18090600	Active TSS	Aorta	Aorta
3	chr17:18085800-18089000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr17:18085800-18089000	Active TSS	Small Intestine	intestine
5	chr17:18085800-18089200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr17:18085800-18089400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:18085800-18090200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr17:18085800-18090600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr17:18086000-18089000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:18086000-18089000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:18086000-18089000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:18086000-18089000	Active TSS	Brain Angular Gyrus	brain
13	chr17:18086000-18089000	Active TSS	Colon Smooth Muscle	Colon
14	chr17:18086000-18089000	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr17:18086000-18089000	Active TSS	Left Ventricle	heart
16	chr17:18086000-18089000	Active TSS	Lung	lung
17	chr17:18086000-18089000	Active TSS	Rectal Smooth Muscle	rectum
18	chr17:18086000-18089000	Active TSS	Hela-S3	cervix
19	chr17:18086000-18089000	Active TSS	HSMM	muscle
20	chr17:18086000-18089200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:18086000-18089200	Active TSS	NHDF-Ad	bronchial
22	chr17:18086000-18089400	Active TSS	GM12878-XiMat	blood
23	chr17:18086000-18090000	Active TSS	Pancreas	Pancrea
24	chr17:18086000-18090200	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr17:18086000-18090200	Active TSS	Ovary	ovary
26	chr17:18086200-18089000	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr17:18086200-18089200	Active TSS	Gastric	stomach
28	chr17:18086200-18089400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:18087400-18089400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:18087400-18089400	Active TSS	Right Atrium	heart
31	chr17:18087600-18089200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:18087600-18090200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr17:18087800-18089000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr17:18087800-18089000	Active TSS	Fetal Heart	heart
35	chr17:18087800-18089200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr17:18087800-18089400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr17:18087800-18089400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
38	chr17:18087800-18089400	Bivalent/Poised TSS	HepG2	liver
39	chr17:18087800-18090400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr17:18087800-18091200	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr17:18087800-18092000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:18087800-18092200	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr17:18088000-18089800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
44	chr17:18088000-18090000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr17:18088000-18090400	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr17:18088000-18090800	Flanking Active TSS	Liver	Liver
47	chr17:18088000-18091200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
48	chr17:18088000-18091800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr17:18088000-18092000	Flanking Active TSS	HUVEC	blood vessel
50	chr17:18088000-18093000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links