Variant report

Variant	rs940336
Chromosome Location	chr7:99032458-99032459
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	chr7:99032285-99032497	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:99030944..99035080-chr7:99035226..99039444,6	MCF-7	breast:
2	chr7:99004079..99005950-chr7:99029849..99032633,2	MCF-7	breast:
3	chr7:99029730..99032537-chr7:99050314..99053165,2	MCF-7	breast:

Variant related genes	Relation type
CPSF4	TF binding region
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1002172	0.84[EUR][1000 genomes]
rs1004387	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10225314	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs10238965	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs10240199	0.82[ASN][1000 genomes]
rs10244158	0.82[ASN][1000 genomes]
rs10254729	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10265385	0.84[ASN][1000 genomes]
rs10271049	0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10279308	0.83[YRI][hapmap]
rs1043466	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10464604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11539770	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772470	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11976018	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12538826	0.99[ASN][1000 genomes]
rs13227795	0.81[ASN][1000 genomes]
rs13240600	0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs13437771	0.81[ASN][1000 genomes]
rs17161652	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17161677	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17161698	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17161766	0.92[EUR][1000 genomes]
rs17161768	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17161769	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17161771	0.84[EUR][1000 genomes]
rs17161772	0.84[EUR][1000 genomes]
rs17161774	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17161780	0.92[EUR][1000 genomes]
rs17161783	0.92[EUR][1000 genomes]
rs1980307	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1985453	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2003499	0.83[YRI][hapmap]
rs2057906	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2107705	1.00[EUR][1000 genomes]
rs2240384	0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2240385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269985	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2272168	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2280600	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2280601	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2404322	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28457808	0.81[ASN][1000 genomes]
rs3137	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs3764815	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3779354	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3800960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3843540	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs45492098	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45540134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45622743	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646446	0.92[EUR][1000 genomes]
rs4646447	0.92[EUR][1000 genomes]
rs4646449	0.92[EUR][1000 genomes]
rs4646453	0.92[EUR][1000 genomes]
rs4646456	0.92[EUR][1000 genomes]
rs58024720	0.84[EUR][1000 genomes]
rs58222677	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58421977	1.00[EUR][1000 genomes]
rs59986060	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60301933	0.87[ASN][1000 genomes]
rs60865030	0.92[EUR][1000 genomes]
rs61159815	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61337492	0.92[EUR][1000 genomes]
rs61402640	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61543997	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6961634	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs6962772	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs72494451	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72494452	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73709637	1.00[EUR][1000 genomes]
rs73709641	1.00[EUR][1000 genomes]
rs7794682	0.86[ASN][1000 genomes]
rs7794705	0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs868564	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs883403	0.83[ASN][1000 genomes]
rs917154	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv888769	chr7:99018584-99041748	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv888770	chr7:99021344-99041748	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99011400-99035000	Weak transcription	Fetal Brain Male	brain
3	chr7:99015600-99035200	Weak transcription	Fetal Kidney	kidney
4	chr7:99015600-99035400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:99015600-99035600	Weak transcription	Stomach Mucosa	stomach
6	chr7:99016800-99036000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:99017600-99035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:99018200-99035200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:99018200-99035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:99018400-99035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:99021400-99034400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:99021600-99035200	Weak transcription	HMEC	breast
13	chr7:99022200-99035400	Weak transcription	NH-A	brain
14	chr7:99023000-99036000	Weak transcription	Small Intestine	intestine
15	chr7:99025600-99033000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:99025600-99033000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr7:99025600-99033000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:99025600-99033000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:99025600-99033200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:99025600-99033200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:99025600-99033400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:99025600-99033400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:99025600-99033800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:99025600-99034400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:99025600-99034800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:99025600-99034800	Strong transcription	Fetal Muscle Leg	muscle
27	chr7:99025600-99035200	Strong transcription	Fetal Stomach	stomach
28	chr7:99025800-99033000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:99025800-99033200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr7:99025800-99034000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:99026000-99032800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:99026000-99032800	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:99026000-99033200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:99026200-99032800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:99026200-99032800	Strong transcription	Colonic Mucosa	Colon
36	chr7:99026200-99032800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr7:99026200-99032800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:99026200-99032800	Strong transcription	Fetal Brain Female	brain
39	chr7:99026200-99032800	Strong transcription	Fetal Thymus	thymus
40	chr7:99026200-99032800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr7:99026200-99033000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr7:99026200-99033000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:99026200-99033000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:99026200-99033000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:99026200-99033000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:99026200-99033000	Strong transcription	Adipose Nuclei	Adipose
47	chr7:99026200-99033000	Strong transcription	Brain Germinal Matrix	brain
48	chr7:99026200-99033000	Strong transcription	Brain Hippocampus Middle	brain
49	chr7:99026200-99033000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr7:99026200-99033200	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links