Variant report

Variant	rs3804440
Chromosome Location	chr5:36158394-36158395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36150277..36153703-chr5:36154371..36162094,13	K562	blood:
2	chr5:36151610..36154488-chr5:36157527..36159493,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145604	Chromatin interaction
ENSG00000164187	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12653480	1.00[AFR][1000 genomes]
rs12653497	1.00[AFR][1000 genomes]
rs12655052	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs13181119	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16902780	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1908391	1.00[AFR][1000 genomes]
rs2270909	0.86[CHB][hapmap]
rs33674	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs35296363	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35338830	1.00[EUR][1000 genomes]
rs35418428	1.00[EUR][1000 genomes]
rs35685853	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789759	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804439	0.89[JPT][hapmap]
rs4869459	1.00[ASW][hapmap]
rs4869460	1.00[AFR][1000 genomes]
rs4869613	1.00[AFR][1000 genomes]
rs4869615	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs4869622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61755301	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	63 gene(s)	inside rSNPs	diseases
2	nsv524075	chr5:36156782-36158394	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36153200-36160800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:36153200-36164000	Weak transcription	Colonic Mucosa	Colon
3	chr5:36153600-36159000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:36153800-36158400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:36153800-36159000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:36153800-36160800	Weak transcription	Gastric	stomach
7	chr5:36153800-36162600	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr5:36153800-36164000	Weak transcription	Pancreas	Pancrea
9	chr5:36153800-36184400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:36154000-36158400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:36154000-36159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:36154000-36160600	Weak transcription	Stomach Mucosa	stomach
13	chr5:36154000-36162000	Genic enhancers	HepG2	liver
14	chr5:36154000-36162600	Genic enhancers	Fetal Intestine Large	intestine
15	chr5:36154000-36168200	Strong transcription	Primary T cells from cord blood	blood
16	chr5:36154000-36168200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:36154000-36175400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:36154000-36175600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr5:36154000-36175600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:36154000-36184200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:36154200-36158800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:36154200-36168400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr5:36154200-36179000	Strong transcription	A549	lung
24	chr5:36154200-36184400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:36154200-36184400	Strong transcription	Fetal Thymus	thymus
26	chr5:36154400-36158800	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr5:36154400-36159000	Genic enhancers	Fetal Brain Female	brain
28	chr5:36154400-36159200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr5:36154400-36162400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:36154400-36164800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:36154400-36175000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr5:36154400-36175200	Strong transcription	Thymus	Thymus
33	chr5:36154400-36184400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:36154400-36210800	Weak transcription	Small Intestine	intestine
35	chr5:36154600-36159000	Weak transcription	Brain Angular Gyrus	brain
36	chr5:36154600-36163200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:36154600-36164000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:36154600-36168000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:36154600-36168200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:36154600-36176000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:36154800-36161600	Weak transcription	Brain Substantia Nigra	brain
42	chr5:36155000-36163600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr5:36155200-36176000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:36155800-36166000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr5:36156000-36158600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr5:36156000-36176400	Strong transcription	Primary B cells from cord blood	blood
47	chr5:36156200-36158600	Genic enhancers	Osteobl	bone
48	chr5:36156200-36159000	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:36156400-36159200	Weak transcription	Brain Anterior Caudate	brain
50	chr5:36156400-36160000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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