Variant report

Variant	rs4727388
Chromosome Location	chr7:97865458-97865459
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	POLR2A	chr7:97865358-97865470	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:97863932..97867672-chr7:97911936..97914933,4	K562	blood:
2	chr7:97844457..97846470-chr7:97865336..97867376,2	MCF-7	breast:
3	chr7:97859627..97861679-chr7:97864267..97867211,3	K562	blood:
4	chr7:97864661..97867509-chr7:97913185..97914838,2	K562	blood:

Variant related genes	Relation type
TECPR1	TF binding region
ENSG00000205356	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10249366	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10953247	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11761574	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11771397	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11771953	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11772438	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11773779	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11984183	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533016	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12539676	0.90[EUR][1000 genomes]
rs12669622	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12704981	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17436977	0.81[CHB][hapmap]
rs2270600	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2270604	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291747	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs2394827	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28566958	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28662014	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4727390	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729421	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56098787	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61575270	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62479836	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62479838	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6951479	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6961129	0.82[CHB][hapmap]
rs6975156	0.81[CHB][hapmap]
rs747631	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747632	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7787309	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7796762	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs954050	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv888763	chr7:97829492-97866291	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv525934	chr7:97853184-97866291	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv1800947	chr7:97857675-97889672	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4727388	GATS	cis	cerebellum	SCAN
rs4727388	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs4727388	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL
rs4727388	TECPR1	cis	parietal	SCAN
rs4727388	FIS1	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97841200-97867800	Weak transcription	HUVEC	blood vessel
2	chr7:97841200-97880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:97841400-97866200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:97841400-97879400	Weak transcription	Fetal Brain Male	brain
5	chr7:97841400-97880200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:97841800-97867400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:97842200-97868400	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:97845200-97877400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr7:97848000-97877600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:97848000-97880600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:97848600-97873200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:97850000-97871800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:97850000-97878000	Strong transcription	Fetal Stomach	stomach
14	chr7:97850200-97874400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr7:97850200-97875400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:97850400-97872800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr7:97850400-97878600	Weak transcription	GM12878-XiMat	blood
18	chr7:97850600-97872800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:97850600-97874400	Strong transcription	Adipose Nuclei	Adipose
20	chr7:97850600-97875600	Strong transcription	Fetal Brain Female	brain
21	chr7:97850800-97875400	Strong transcription	Thymus	Thymus
22	chr7:97850800-97877400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:97851600-97867600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:97851800-97867600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:97852000-97878000	Weak transcription	Small Intestine	intestine
26	chr7:97852600-97875600	Strong transcription	Primary T cells from cord blood	blood
27	chr7:97853200-97880000	Weak transcription	A549	lung
28	chr7:97853400-97880200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:97854000-97869800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr7:97854400-97870800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:97856000-97866800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:97856200-97867400	Weak transcription	Fetal Lung	lung
33	chr7:97857000-97879000	Strong transcription	Brain Germinal Matrix	brain
34	chr7:97857800-97867400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:97858000-97867400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:97858200-97878200	Weak transcription	Stomach Mucosa	stomach
37	chr7:97858200-97879000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:97858800-97866200	Weak transcription	Osteobl	bone
39	chr7:97858800-97874600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:97859000-97867400	Weak transcription	HSMMtube	muscle
41	chr7:97859200-97867400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:97859200-97880200	Weak transcription	Psoas Muscle	Psoas
43	chr7:97859800-97878200	Weak transcription	HepG2	liver
44	chr7:97860200-97871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:97860200-97871800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr7:97860200-97875600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr7:97860200-97878400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr7:97860400-97867200	Weak transcription	Fetal Thymus	thymus
49	chr7:97861200-97869200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr7:97861600-97870200	Weak transcription	Dnd41	blood

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