Variant report

Variant	rs3968877
Chromosome Location	chr5:74070492-74070493
allele	A/G
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	chr5:74070446-74070893	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:74070106..74071963-chr5:74087987..74090742,2	K562	blood:
2	chr5:74070152..74072138-chr5:74074887..74076433,2	K562	blood:
3	chr5:74063024..74065513-chr5:74069394..74071434,2	K562	blood:
4	chr5:74063430..74066095-chr5:74068768..74070600,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-1330P	TF binding region
ENSG00000164346	Chromatin interaction
ENSG00000199645	Chromatin interaction
ENSG00000164347	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10062244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1043968	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10515189	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10515191	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11556477	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739122	1.00[JPT][hapmap]
rs11740871	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11741464	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11741789	1.00[JPT][hapmap]
rs11741825	0.81[ASN][1000 genomes]
rs11742460	0.81[ASN][1000 genomes]
rs11743415	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11743655	0.90[JPT][hapmap]
rs11746069	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11746611	0.90[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11746702	0.82[JPT][hapmap]
rs11746717	0.89[ASN][1000 genomes]
rs11747965	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11749137	1.00[JPT][hapmap]
rs11948188	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11955898	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1350097	1.00[JPT][hapmap]
rs1447453	1.00[JPT][hapmap]
rs1531103	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs15694	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs16872269	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs16872297	0.82[ASN][1000 genomes]
rs16872299	0.82[JPT][hapmap]
rs16872346	1.00[JPT][hapmap]
rs16872352	0.91[YRI][hapmap]
rs17670605	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17670701	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17670867	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17670897	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17670975	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17671140	0.89[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs17738111	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17738266	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17738565	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17738645	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17738674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17852781	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1992712	0.81[CEU][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1993370	1.00[JPT][hapmap]
rs1993372	0.84[ASN][1000 genomes]
rs2044410	1.00[JPT][hapmap]
rs2061162	1.00[JPT][hapmap]
rs2084115	0.81[ASN][1000 genomes]
rs2084119	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2166361	0.81[ASN][1000 genomes]
rs2314936	0.82[ASN][1000 genomes]
rs2314937	0.82[ASN][1000 genomes]
rs34496480	0.81[ASN][1000 genomes]
rs3733794	1.00[JPT][hapmap]
rs3932895	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5020673	0.84[ASN][1000 genomes]
rs55870102	0.82[ASN][1000 genomes]
rs56276104	0.82[ASN][1000 genomes]
rs56365996	0.82[ASN][1000 genomes]
rs58184895	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58367004	0.82[ASN][1000 genomes]
rs59110717	0.82[ASN][1000 genomes]
rs61093699	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62366373	0.81[ASN][1000 genomes]
rs62366375	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62366376	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62366406	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62366408	0.80[ASN][1000 genomes]
rs62366413	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62366415	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62366416	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62366417	0.82[ASN][1000 genomes]
rs62366418	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62366419	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62366420	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62366421	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62366450	0.84[ASN][1000 genomes]
rs62366453	0.84[ASN][1000 genomes]
rs62366454	0.84[ASN][1000 genomes]
rs62366456	0.82[ASN][1000 genomes]
rs62366457	0.84[ASN][1000 genomes]
rs62366459	0.84[ASN][1000 genomes]
rs62367762	0.82[ASN][1000 genomes]
rs62367765	0.84[ASN][1000 genomes]
rs6453077	0.82[JPT][hapmap]
rs6453084	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6453086	1.00[JPT][hapmap]
rs6453087	1.00[JPT][hapmap]
rs6859014	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6861730	0.81[ASN][1000 genomes]
rs6863738	0.84[ASN][1000 genomes]
rs6866082	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6874609	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6877116	1.00[JPT][hapmap]
rs6877442	1.00[JPT][hapmap]
rs6879781	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6882499	1.00[JPT][hapmap]
rs6883061	1.00[JPT][hapmap]
rs6884843	1.00[JPT][hapmap]
rs6885093	0.82[JPT][hapmap]
rs6885675	1.00[JPT][hapmap]
rs6897698	1.00[JPT][hapmap]
rs72764666	0.82[ASN][1000 genomes]
rs72764681	0.84[ASN][1000 genomes]
rs73116712	0.85[AFR][1000 genomes]
rs73116717	0.80[AFR][1000 genomes]
rs73120619	0.81[ASN][1000 genomes]
rs7708203	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7728889	1.00[JPT][hapmap]
rs820825	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs820827	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820828	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs820830	0.90[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820832	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820833	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs820834	0.80[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs820835	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9686657	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv968948	chr5:74069688-74072622	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74064000-74071000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:74064000-74076000	Weak transcription	Esophagus	oesophagus
3	chr5:74064000-74077200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:74064000-74112400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:74064200-74070600	Weak transcription	Pancreas	Pancrea
6	chr5:74064200-74073000	Weak transcription	Gastric	stomach
7	chr5:74064200-74073800	Weak transcription	Small Intestine	intestine
8	chr5:74064200-74076000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:74064200-74086000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:74064200-74102000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:74064400-74073800	Weak transcription	Stomach Mucosa	stomach
12	chr5:74064400-74076600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:74064400-74079600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:74064400-74086600	Weak transcription	Fetal Heart	heart
15	chr5:74064400-74134600	Weak transcription	Fetal Brain Male	brain
16	chr5:74064600-74074400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:74064600-74079400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:74064600-74079600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:74064800-74072400	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:74064800-74074000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:74064800-74074400	Strong transcription	Osteobl	bone
22	chr5:74064800-74074600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:74064800-74074600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:74064800-74074600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:74064800-74074800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:74064800-74074800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:74064800-74075000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:74064800-74075000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr5:74064800-74075000	Strong transcription	NH-A	brain
30	chr5:74064800-74079400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:74064800-74079600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:74064800-74080000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr5:74064800-74080400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:74064800-74101200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:74065000-74070800	Strong transcription	NHDF-Ad	bronchial
36	chr5:74065000-74072000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr5:74065000-74072000	Strong transcription	Brain Germinal Matrix	brain
38	chr5:74065000-74072000	Strong transcription	Fetal Muscle Leg	muscle
39	chr5:74065000-74072400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:74065000-74072400	Strong transcription	Primary T cells from cord blood	blood
41	chr5:74065000-74072400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:74065000-74072600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:74065000-74072600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:74065000-74073000	Strong transcription	Fetal Lung	lung
45	chr5:74065000-74074000	Strong transcription	Fetal Intestine Large	intestine
46	chr5:74065000-74074200	Strong transcription	Placenta	Placenta
47	chr5:74065000-74074400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:74065000-74074800	Strong transcription	Fetal Thymus	thymus
49	chr5:74065000-74074800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr5:74065000-74077800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links