Variant report

Variant	rs1561716
Chromosome Location	chr8:96145800-96145801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:380)
CpG islands
(count:61)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:380 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB33	chr8:96145524-96146249	HCT-116	colon:	n/a	chr8:96145783-96145793
2	GTF2F1	chr8:96145565-96146230	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA3	chr8:96145326-96145920	T-47D	breast:	n/a	n/a
4	POLR2A	chr8:96145725-96146449	GM12878	blood:	n/a	n/a
5	SRF	chr8:96145463-96146299	MCF-7	breast:	n/a	chr8:96145895-96145905 chr8:96146050-96146060
6	SMARCB1	chr8:96145508-96146803	Hela-S3	cervix:	n/a	n/a
7	NR2F2	chr8:96145332-96147229	MCF-7	breast:	n/a	n/a
8	FOXA1	chr8:96145685-96146321	HepG2	liver:	n/a	n/a
9	CTCF	chr8:96145733-96145827	NHEK	skin:	n/a	n/a
10	POLR2A	chr8:96145627-96146479	Gliobla	brain:	n/a	n/a
11	CTCF	chr8:96145764-96145815	MCF-7	breast:	n/a	n/a
12	POLR2A	chr8:96145555-96146507	MCF-7	breast:	n/a	n/a
13	ZBTB7A	chr8:96145773-96146933	ECC-1	luminal epithelium:	n/a	n/a
14	FOXP2	chr8:96145696-96146325	PFSK-1	brain:	n/a	n/a
15	GATA3	chr8:96145228-96146493	MCF-7	breast:	n/a	chr8:96145307-96145314
16	TEAD4	chr8:96145568-96146317	K562	blood:	n/a	n/a
17	POLR2A	chr8:96145575-96146405	K562	blood:	n/a	n/a
18	MAX	chr8:96145509-96146371	SK-N-SH	brain:	n/a	chr8:96145980-96145990
19	USF2	chr8:96145435-96145986	Hela-S3	cervix:	n/a	n/a
20	SIN3AK20	chr8:96145240-96146481	MCF-7	breast:	n/a	n/a
21	MAX	chr8:96145208-96146329	MCF-7	breast:	n/a	chr8:96145980-96145990
22	PML	chr8:96145388-96146410	K562	blood:	n/a	n/a
23	ELF1	chr8:96145739-96146411	K562	blood:	n/a	chr8:96146386-96146398 chr8:96146358-96146370
24	YY1	chr8:96145672-96145866	K562	blood:	n/a	n/a
25	EP300	chr8:96145382-96146255	T-47D	breast:	n/a	chr8:96146118-96146134 chr8:96146119-96146135 chr8:96146065-96146081
26	HEY1	chr8:96145575-96146480	K562	blood:	n/a	chr8:96146115-96146130 chr8:96146071-96146086 chr8:96145819-96145834 chr8:96145958-96145973
27	ZNF143	chr8:96145614-96146381	Hela-S3	cervix:	n/a	chr8:96146358-96146368 chr8:96145819-96145829
28	RAD21	chr8:96145276-96146150	MCF-7	breast:	n/a	chr8:96146122-96146135
29	SPI1	chr8:96145783-96145982	K562	blood:	n/a	chr8:96145903-96145916
30	TAF1	chr8:96145562-96146598	ECC-1	luminal epithelium:	n/a	n/a
31	USF1	chr8:96145548-96145951	H1-hESC	embryonic stem cell:	n/a	n/a
32	E2F6	chr8:96144862-96146609	H1-hESC	embryonic stem cell:	n/a	chr8:96145986-96145995 chr8:96146115-96146125 chr8:96145854-96145861
33	FOS	chr8:96145609-96145913	MCF10A-Er-Src	breast:	n/a	n/a
34	SMC3	chr8:96145506-96146378	Hela-S3	cervix:	n/a	chr8:96146199-96146207
35	MYBL2	chr8:96145543-96146348	HepG2	liver:	n/a	n/a
36	MBD4	chr8:96145497-96145967	HepG2	liver:	n/a	n/a
37	MXI1	chr8:96145047-96146164	H1-hESC	embryonic stem cell:	n/a	n/a
38	BHLHE40	chr8:96145385-96146234	HepG2	liver:	n/a	n/a
39	POLR2A	chr8:96145587-96146424	Hela-S3	cervix:	n/a	n/a
40	E2F6	chr8:96145320-96146210	H1-hESC	embryonic stem cell:	n/a	chr8:96145986-96145995 chr8:96146115-96146125 chr8:96145854-96145861
41	POLR2A	chr8:96145612-96146769	GM12892	blood:	n/a	n/a
42	TBP	chr8:96145560-96146444	K562	blood:	n/a	n/a
43	POLR2A	chr8:96145617-96146407	HCT-116	colon:	n/a	n/a
44	POLR2A	chr8:96145512-96146420	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr8:96145568-96146401	HepG2	liver:	n/a	n/a
46	POLR2A	chr8:96145474-96146397	K562	blood:	n/a	n/a
47	EP300	chr8:96145798-96146242	HepG2	liver:	n/a	chr8:96146118-96146134 chr8:96146119-96146135 chr8:96146065-96146081
48	TAF1	chr8:96145730-96146529	GM12878	blood:	n/a	n/a
49	TAF1	chr8:96145726-96146470	K562	blood:	n/a	n/a
50	RAD21	chr8:96145401-96146377	ECC-1	luminal epithelium:	n/a	chr8:96146122-96146135

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:96145761-96145811	NT2-D1	testis:	n/a
2	chr8:96145761-96145811	AG09309	skin:	n/a
3	chr8:96145761-96145811	HPAEpiC	pulmonary alveolar:	n/a
4	chr8:96145761-96145811	ovcar-3	ovarian:	n/a
5	chr8:96145761-96145811	RPTEC	kidney:	n/a
6	chr8:96145761-96145811	A549	lung:	n/a
7	chr8:96145761-96145811	HAEpiC	amniotic membrane:	n/a
8	chr8:96145761-96145811	LNCaP	prostate:	n/a
9	chr8:96145761-96145811	NH-A	brain:	n/a
10	chr8:96145761-96145811	AG04450	lung:	fetal
11	chr8:96145761-96145811	HEEpiC	esophagus:	n/a
12	chr8:96145761-96145811	MCF10A-Er-Src	breast:	n/a
13	chr8:96145761-96145811	SK-N-SH_RA	brain:	n/a
14	chr8:96145761-96145811	GM12892	blood:	n/a
15	chr8:96145761-96145811	PANC-1	pancreas:	n/a
16	chr8:96145761-96145811	HNPCEpiC	eye:	n/a
17	chr8:96145761-96145811	T-47D	breast:	n/a
18	chr8:96145761-96145811	SAEC	small airway:	n/a
19	chr8:96145761-96145811	IMR90	lung:	fetal
20	chr8:96145761-96145811	Caco-2	colon:	n/a
21	chr8:96145761-96145811	PFSK-1	brain:	n/a
22	chr8:96145761-96145811	HRCEpiC	kidney:	n/a
23	chr8:96145761-96145811	HRE	kidney:	n/a
24	chr8:96145761-96145811	HCM	heart:	n/a
25	chr8:96145761-96145811	AG10803	skin:	n/a
26	chr8:96145761-96145811	BE2_C	brain:	n/a
27	chr8:96145761-96145811	BJ	skin:	n/a
28	chr8:96145761-96145811	SK-N-SH	brain:	n/a
29	chr8:96145761-96145811	AG09319	gingival:	n/a
30	chr8:96145761-96145811	HepG2	liver:	n/a
31	chr8:96145761-96145811	ProgFib	skin:	n/a
32	chr8:96145761-96145811	HUVEC	blood vessel:	n/a
33	chr8:96145761-96145811	NB4	blood:	n/a
34	chr8:96145761-96145811	H1-hESC	embryonic stem cell:	embryo
35	chr8:96145761-96145811	HCPEpiC	choroid plexus:	n/a
36	chr8:96145761-96145811	PrEC	prostate:	n/a
37	chr8:96145761-96145811	Hela-S3	cervix:	n/a
38	chr8:96145761-96145811	AoSMC	blood vessel:	n/a
39	chr8:96145761-96145811	GM12878	blood:	n/a
40	chr8:96145761-96145811	MCF-7	breast:	n/a
41	chr8:96145761-96145811	CMK	blood:	n/a
42	chr8:96145761-96145811	NHBE	bronchial:	n/a
43	chr8:96145761-96145811	GM12891	blood:	n/a
44	chr8:96145761-96145811	HEK293	kidney:	embryo
45	chr8:96145761-96145811	Jurkat	blood:	n/a
46	chr8:96145761-96145811	AG04449	skin:	fetal
47	chr8:96145761-96145811	NHDF-neo	bronchial:	n/a
48	chr8:96145761-96145811	HMEC	breast:	n/a
49	chr8:96145761-96145811	K562	blood:	n/a
50	chr8:96145761-96145811	HIPEpiC	eye:	n/a

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:96095758..96103345-chr8:96144049..96152228,17	MCF-7	breast:
2	chr8:96064790..96067980-chr8:96145061..96147723,3	MCF-7	breast:
3	chr17:57181515..57184136-chr8:96145563..96147575,2	MCF-7	breast:
4	chr8:95958803..95961918-chr8:96144805..96148535,6	MCF-7	breast:
5	chr8:95959198..95962585-chr8:96144089..96147312,4	MCF-7	breast:
6	chr8:96142341..96149648-chr8:96278644..96282772,12	MCF-7	breast:
7	chr14:51410376..51411320-chr8:96145334..96146212,2	Hela-S3	cervix:
8	chr8:96144909..96147734-chr8:96280323..96283069,4	K562	blood:
9	chr8:96066564..96073895-chr8:96144947..96151399,9	MCF-7	breast:
10	chr8:96131679..96134773-chr8:96142918..96145954,3	MCF-7	breast:
11	chr8:96107778..96115564-chr8:96144421..96149353,22	MCF-7	breast:
12	chr8:96143208..96147491-chr8:96279441..96282856,8	MCF-7	breast:
13	chr8:96060626..96064106-chr8:96144836..96147979,3	MCF-7	breast:
14	chr8:96085590..96087361-chr8:96143254..96146025,2	K562	blood:
15	chr8:96081666..96087784-chr8:96143058..96146914,11	MCF-7	breast:
16	chr8:96108471..96116302-chr8:96144708..96150629,15	MCF-7	breast:
17	chr8:96096484..96101537-chr8:96142870..96147410,9	MCF-7	breast:
18	chr8:95906813..95909487-chr8:96144078..96147982,7	MCF-7	breast:
19	chr8:95906396..95909110-chr8:96144664..96147276,2	MCF-7	breast:
20	chr8:96035216..96038805-chr8:96144544..96148215,5	MCF-7	breast:
21	chr8:95906309..95909766-chr8:96145150..96148465,4	K562	blood:
22	chr8:96082201..96091738-chr8:96143838..96148400,13	MCF-7	breast:
23	chr17:59477291..59479669-chr8:96145065..96147248,2	MCF-7	breast:
24	chr8:96035638..96037575-chr8:96142596..96146380,3	K562	blood:
25	chr8:96033821..96037970-chr8:96145284..96149341,6	MCF-7	breast:
26	chr8:96145549..96147076-chr8:97273439..97275533,2	MCF-7	breast:
27	chr8:95908266..95910460-chr8:96145570..96147664,2	K562	blood:

No data

Variant related genes	Relation type
PLEKHF2	TF binding region
PLEKHF2	CpG island
ENSG00000175305	Chromatin interaction
ENSG00000245080	Chromatin interaction
ENSG00000253878	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000200525	Chromatin interaction
ENSG00000254248	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000156170	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000253773	Chromatin interaction
ENSG00000164938	Chromatin interaction
ENSG00000156471	Chromatin interaction
ENSG00000100504	Chromatin interaction
ENSG00000156172	Chromatin interaction
ENSG00000156469	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10088488	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10092259	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10099012	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10101612	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10109640	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10956939	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11985227	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11987616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11989019	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11994118	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12334474	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12335131	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28417924	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28431240	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28470215	0.84[EUR][1000 genomes]
rs28512193	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28704607	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58419720	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58536083	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60144755	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7827540	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7842028	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7842334	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv891207	chr8:96106037-96160914	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	esv3371147	chr8:96145201-96147749	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:177 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96145000-96145800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:96145000-96145800	Flanking Active TSS	NHEK	skin
3	chr8:96145000-96147400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr8:96145000-96147400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr8:96145000-96147600	Active TSS	Brain Anterior Caudate	brain
6	chr8:96145000-96147800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr8:96145200-96145800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr8:96145200-96145800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr8:96145200-96145800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr8:96145200-96145800	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr8:96145200-96145800	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr8:96145200-96145800	Flanking Active TSS	Fetal Lung	lung
13	chr8:96145200-96145800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr8:96145200-96145800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr8:96145200-96145800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr8:96145200-96145800	Flanking Active TSS	Dnd41	blood
17	chr8:96145200-96145800	Flanking Active TSS	GM12878-XiMat	blood
18	chr8:96145200-96145800	Flanking Active TSS	K562	blood
19	chr8:96145200-96145800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr8:96145200-96145800	Flanking Active TSS	NH-A	brain
21	chr8:96145200-96146800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr8:96145200-96147200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr8:96145200-96147200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:96145200-96147200	Active TSS	Brain Cingulate Gyrus	brain
25	chr8:96145200-96147200	Active TSS	Osteobl	bone
26	chr8:96145200-96147400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr8:96145200-96147400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr8:96145200-96147400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:96145200-96147400	Active TSS	Colon Smooth Muscle	Colon
30	chr8:96145200-96147400	Active TSS	Placenta Amnion	Placenta Amnion
31	chr8:96145200-96147600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr8:96145200-96147600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr8:96145200-96147600	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr8:96145200-96147800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr8:96145200-96147800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr8:96145200-96148000	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr8:96145200-96148200	Active TSS	Psoas Muscle	Psoas
38	chr8:96145200-96148400	Active TSS	Colonic Mucosa	Colon
39	chr8:96145200-96148400	Active TSS	Fetal Kidney	kidney
40	chr8:96145200-96148400	Active TSS	Fetal Muscle Trunk	muscle
41	chr8:96145200-96150000	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr8:96145400-96145800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr8:96145400-96145800	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr8:96145400-96145800	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr8:96145400-96145800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr8:96145400-96145800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr8:96145400-96145800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr8:96145400-96145800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr8:96145400-96145800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr8:96145400-96145800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links