Variant report

Variant	rs13095863
Chromosome Location	chr3:43334878-43334879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43326351..43330245-chr3:43331873..43336524,8	MCF-7	breast:
2	chr3:43332997..43335477-chr3:43335619..43338331,2	K562	blood:
3	chr3:43327270..43330892-chr3:43331691..43335794,4	K562	blood:

Variant related genes	Relation type
ENSG00000163788	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12485977	0.92[ASN][1000 genomes]
rs12492694	1.00[YRI][hapmap]
rs1588026	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17075317	0.85[JPT][hapmap]
rs34823561	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4128530	1.00[YRI][hapmap]
rs6793392	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7621298	0.91[ASW][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9681394	0.85[JPT][hapmap]
rs9683242	0.82[JPT][hapmap]
rs9817430	0.86[AMR][1000 genomes]
rs9858494	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9862259	0.91[ASW][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]

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	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv876732	chr3:43326887-43360879	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv590155	chr3:43327873-43334878	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv590158	chr3:43327924-43334878	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv590160	chr3:43328076-43334878	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13095863	CCBP2	cis	cerebellum	SCAN
rs13095863	TMEM42	cis	cerebellum	SCAN
rs13095863	ZNF620	cis	parietal	SCAN
rs13095863	CXCR6	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43329200-43344800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:43329200-43346800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:43329400-43346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:43329600-43345000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:43329800-43335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:43330400-43344800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:43330800-43336400	Weak transcription	HSMMtube	muscle
8	chr3:43330800-43344600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:43330800-43359000	Weak transcription	Fetal Brain Male	brain
10	chr3:43331000-43335400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:43331000-43340600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:43331000-43344600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:43331200-43338200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:43331200-43344600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:43331400-43338000	Weak transcription	HSMM	muscle
16	chr3:43331400-43338000	Weak transcription	K562	blood
17	chr3:43331400-43344600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:43331400-43344600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:43331400-43358200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:43331600-43335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:43331600-43338200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:43331600-43338200	Weak transcription	Brain Angular Gyrus	brain
23	chr3:43331600-43344600	Weak transcription	Placenta	Placenta
24	chr3:43331600-43344600	Weak transcription	Hela-S3	cervix
25	chr3:43331600-43344800	Weak transcription	Brain Germinal Matrix	brain
26	chr3:43331800-43339600	Enhancers	Liver	Liver
27	chr3:43332000-43336000	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr3:43332200-43335000	Enhancers	Fetal Heart	heart
29	chr3:43332400-43361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:43332600-43335400	Enhancers	Colon Smooth Muscle	Colon
31	chr3:43332600-43336200	Weak transcription	A549	lung
32	chr3:43332600-43336600	Enhancers	Primary B cells from cord blood	blood
33	chr3:43332800-43335000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:43332800-43335000	Enhancers	HepG2	liver
35	chr3:43332800-43336000	Weak transcription	Fetal Kidney	kidney
36	chr3:43332800-43336800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:43332800-43338000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:43332800-43338000	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:43332800-43338200	Weak transcription	Aorta	Aorta
40	chr3:43332800-43339600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:43332800-43339600	Weak transcription	Colonic Mucosa	Colon
42	chr3:43332800-43377000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:43333000-43335000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:43333000-43335200	Enhancers	Adipose Nuclei	Adipose
45	chr3:43333000-43336000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:43333000-43336000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:43333000-43336400	Weak transcription	Fetal Intestine Large	intestine
48	chr3:43333000-43336400	Weak transcription	Fetal Intestine Small	intestine
49	chr3:43333000-43336600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:43333000-43336600	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links