Variant report

Variant	rs4678436
Chromosome Location	chr3:136317402-136317403
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136317046..136319207-chr3:136469829..136472283,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1017882	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10935185	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935186	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11919030	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12163529	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2688600	0.84[AMR][1000 genomes]
rs2688601	0.84[AMR][1000 genomes]
rs34438032	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4038587	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4521165	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4630889	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55970317	0.90[AMR][1000 genomes]
rs6439649	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6791142	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6808312	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73228043	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7427564	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7432375	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7618518	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7637129	0.81[ASN][1000 genomes]
rs940174	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1794138	chr3:136300732-136332204	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4678436	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
5	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:136251600-136322400	Weak transcription	Liver	Liver
8	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
11	chr3:136271200-136331400	Weak transcription	NHDF-Ad	bronchial
12	chr3:136272600-136335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:136280000-136323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:136283800-136341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:136284400-136337800	Weak transcription	Fetal Kidney	kidney
16	chr3:136285200-136335400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:136286800-136322600	Weak transcription	Placenta	Placenta
18	chr3:136286800-136343600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:136287200-136335400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:136289600-136341800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:136290000-136351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:136294800-136319600	Weak transcription	Fetal Lung	lung
23	chr3:136297200-136345400	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:136297200-136351200	Weak transcription	Pancreas	Pancrea
25	chr3:136298600-136351600	Weak transcription	HSMM	muscle
26	chr3:136300000-136335400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:136300200-136351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:136304800-136318600	Weak transcription	Fetal Intestine Large	intestine
29	chr3:136304800-136331200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:136304800-136331400	Weak transcription	NHLF	lung
31	chr3:136305000-136320400	Weak transcription	Adipose Nuclei	Adipose
32	chr3:136305200-136339400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:136305800-136318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:136305800-136322200	Weak transcription	Hela-S3	cervix
35	chr3:136305800-136338000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:136305800-136343800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:136306000-136341400	Weak transcription	Stomach Mucosa	stomach
38	chr3:136306200-136319000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:136306200-136327800	Weak transcription	Gastric	stomach
40	chr3:136306200-136341800	Weak transcription	Fetal Brain Female	brain
41	chr3:136306200-136343400	Weak transcription	HepG2	liver
42	chr3:136306800-136327000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:136308000-136319200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:136308000-136321400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:136308000-136327200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:136308000-136357400	Weak transcription	Lung	lung
47	chr3:136308400-136319400	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:136308800-136319400	Weak transcription	Fetal Stomach	stomach
49	chr3:136309000-136319200	Weak transcription	Fetal Intestine Small	intestine
50	chr3:136311000-136324000	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links