Variant report

Variant	rs7676504
Chromosome Location	chr4:99817514-99817515
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	chr4:99817455-99817573	Gliobla	brain:	n/a	n/a
2	POLR2A	chr4:99817484-99817590	MCF-7	breast:	n/a	n/a
3	POLR2A	chr4:99817278-99817757	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr4:99817490-99817541	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99815975..99818089-chr4:99818549..99820506,2	MCF-7	breast:
2	chr4:99815882..99818717-chr4:99847695..99851571,3	K562	blood:

Variant related genes	Relation type
EIF4E	TF binding region
ENSG00000263923	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000151247	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10007957	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10008093	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10010610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10011791	0.91[ASN][1000 genomes]
rs10019506	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10020687	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10022521	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10032966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10212891	0.90[ASN][1000 genomes]
rs1036946	1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10433891	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs10433976	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10461135	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10470955	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10516437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11725932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11728783	0.98[ASN][1000 genomes]
rs11737130	0.97[ASN][1000 genomes]
rs11737186	0.97[ASN][1000 genomes]
rs1230147	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230149	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1230150	0.89[ASN][1000 genomes]
rs1230152	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1230189	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs13110531	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17028238	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17028241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17028244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17028293	0.94[ASN][1000 genomes]
rs17550514	0.98[ASN][1000 genomes]
rs2602889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28367437	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28376834	0.95[ASN][1000 genomes]
rs28430857	0.99[ASN][1000 genomes]
rs28473608	0.98[ASN][1000 genomes]
rs28499420	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28529446	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28575093	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28577966	0.99[ASN][1000 genomes]
rs28589528	0.91[ASN][1000 genomes]
rs28613604	0.99[ASN][1000 genomes]
rs28622595	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28633499	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3133161	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35447189	0.89[ASN][1000 genomes]
rs4699368	0.87[CEU][hapmap]
rs4699370	0.81[ASN][1000 genomes]
rs60120090	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60658326	0.98[ASN][1000 genomes]
rs6532774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6830125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6841295	0.99[ASN][1000 genomes]
rs6846266	0.99[ASN][1000 genomes]
rs6846475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs72677504	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72692622	1.00[ASN][1000 genomes]
rs7660937	0.97[ASN][1000 genomes]
rs7661487	0.94[ASN][1000 genomes]
rs7664964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7666015	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7671306	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7679685	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7684964	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7696573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7696584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7697071	0.99[ASN][1000 genomes]
rs9332467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs994636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995478	0.90[ASN][1000 genomes]
rs9996959	0.94[ASN][1000 genomes]
rs9998221	0.83[AMR][1000 genomes]
rs9999702	0.91[ASN][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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv879655	chr4:99783733-99843113	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv821288	chr4:99813093-99818986	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv819967	chr4:99813509-99817841	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv20331	chr4:99813534-99818241	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99792400-99825000	Weak transcription	Gastric	stomach
2	chr4:99796000-99826400	Weak transcription	Right Ventricle	heart
3	chr4:99797000-99826600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:99798400-99823000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:99798600-99824400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:99799000-99823000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr4:99799800-99823200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:99800200-99823400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:99800400-99823200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:99800600-99824200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr4:99801600-99829400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:99802200-99824000	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:99802600-99823800	Strong transcription	Fetal Thymus	thymus
14	chr4:99802600-99824400	Strong transcription	Dnd41	blood
15	chr4:99802800-99819600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:99802800-99824600	Weak transcription	Pancreas	Pancrea
17	chr4:99802800-99830200	Weak transcription	Ovary	ovary
18	chr4:99802800-99849000	Weak transcription	Aorta	Aorta
19	chr4:99803000-99825000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:99803200-99824200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:99804400-99848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:99804600-99838400	Weak transcription	Esophagus	oesophagus
23	chr4:99804800-99820600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:99805000-99823200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:99805200-99832000	Weak transcription	Spleen	Spleen
26	chr4:99807200-99849000	Weak transcription	Colonic Mucosa	Colon
27	chr4:99807400-99822000	Weak transcription	Hela-S3	cervix
28	chr4:99807400-99826400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:99807600-99824000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:99807800-99817800	Weak transcription	Lung	lung
31	chr4:99807800-99822200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:99807800-99822400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:99807800-99832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:99808000-99822000	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:99808000-99841400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:99808400-99819200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:99808600-99821800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:99808600-99822000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:99808600-99830600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:99808600-99849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:99808800-99822400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr4:99809800-99823600	Strong transcription	GM12878-XiMat	blood
43	chr4:99812200-99826400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:99812600-99820800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr4:99812600-99822000	Weak transcription	NHEK	skin
46	chr4:99812600-99823800	Weak transcription	Fetal Heart	heart
47	chr4:99812800-99824400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:99813400-99818400	Strong transcription	K562	blood
49	chr4:99813400-99823400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:99813400-99825800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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