Variant report

Variant	rs3805487
Chromosome Location	chr5:40796033-40796034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40793843..40796817-chr5:40803354..40805786,3	K562	blood:
2	chr5:40753118..40757884-chr5:40795999..40799979,7	MCF-7	breast:
3	chr5:40755012..40759487-chr5:40796000..40799940,8	K562	blood:
4	chr5:40773088..40775822-chr5:40794513..40796616,2	MCF-7	breast:
5	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
6	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113638	Chromatin interaction
ENSG00000145592	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1001684	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1002423	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1002424	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10041430	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10071679	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10074991	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122655	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11956019	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11956047	0.89[AMR][1000 genomes]
rs11957736	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13361707	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329353	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28544962	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805495	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805497	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4957352	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58692207	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58751240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59133000	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59338019	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59585832	0.97[ASN][1000 genomes]
rs6868517	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7702883	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7705504	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756200-40797200	Weak transcription	Gastric	stomach
2	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
4	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
6	chr5:40777000-40796600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:40777000-40796600	Weak transcription	Thymus	Thymus
8	chr5:40777000-40796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:40777000-40797000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:40777200-40796600	Weak transcription	Fetal Thymus	thymus
11	chr5:40777200-40796800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:40777800-40796600	Weak transcription	NH-A	brain
13	chr5:40781000-40796800	Weak transcription	Aorta	Aorta
14	chr5:40788400-40796600	Weak transcription	Brain Anterior Caudate	brain
15	chr5:40788600-40796600	Weak transcription	Fetal Kidney	kidney
16	chr5:40788800-40796400	Weak transcription	Fetal Brain Female	brain
17	chr5:40788800-40796400	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:40788800-40796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:40788800-40796600	Weak transcription	Fetal Stomach	stomach
20	chr5:40788800-40797400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:40789000-40796600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:40789200-40796600	Weak transcription	Brain Germinal Matrix	brain
23	chr5:40789600-40796600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:40789800-40796800	Weak transcription	Fetal Heart	heart
25	chr5:40790400-40797200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:40790600-40797200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:40791800-40796400	Weak transcription	NHEK	skin
28	chr5:40791800-40796600	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:40792000-40796400	Weak transcription	HMEC	breast
30	chr5:40792000-40796600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:40792000-40796600	Weak transcription	Right Atrium	heart
32	chr5:40792000-40796600	Weak transcription	HSMMtube	muscle
33	chr5:40792200-40796400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:40792400-40796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:40792400-40796600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:40792400-40796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:40792600-40796600	Weak transcription	Colon Smooth Muscle	Colon
38	chr5:40793000-40796400	Enhancers	HepG2	liver
39	chr5:40793600-40796400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:40793600-40796800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:40793800-40797000	Weak transcription	Brain Substantia Nigra	brain
42	chr5:40794000-40796400	Weak transcription	Primary T cells from cord blood	blood
43	chr5:40794000-40796400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:40794200-40797200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr5:40794400-40796200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:40795200-40796200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:40795200-40796200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr5:40795200-40796400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr5:40795200-40796600	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr5:40795200-40796600	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links