Variant report

Variant	rs7632449
Chromosome Location	chr3:101389193-101389194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101387758..101391620-chr3:101393894..101396979,5	MCF-7	breast:
2	chr3:101381844..101383869-chr3:101386784..101389655,2	MCF-7	breast:
3	chr3:101388186..101389836-chr3:101391402..101393014,2	K562	blood:
4	chr3:101388785..101391270-chr3:101393939..101397266,4	MCF-7	breast:
5	chr3:101388568..101391346-chr3:101393644..101398339,4	K562	blood:

Variant related genes	Relation type
ENSG00000256628	Chromatin interaction
ENSG00000066422	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1078154	1.00[YRI][hapmap]
rs12629395	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13065665	0.88[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs13078121	0.88[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs13097625	0.84[MEX][hapmap];0.81[MKK][hapmap]
rs16844120	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625288	0.84[YRI][hapmap]
rs34103639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34408425	0.82[AFR][1000 genomes]
rs34508490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35102530	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610988	0.85[EUR][1000 genomes]
rs6441619	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6762367	1.00[YRI][hapmap]
rs6791241	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792847	0.87[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71315245	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71315246	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71315249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619122	0.82[AFR][1000 genomes]
rs7630598	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637805	0.82[AFR][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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7632449	NIT2	cis	cerebellum	SCAN
rs7632449	ZBTB11	cis	cerebellum	SCAN
rs7632449	CBLB	cis	cerebellum	SCAN
rs7632449	C3orf26	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101362800-101391600	Weak transcription	Stomach Mucosa	stomach
2	chr3:101363000-101394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:101363200-101394400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:101363400-101391400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:101364800-101391000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:101364800-101391000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:101364800-101392000	Strong transcription	Primary T cells from cord blood	blood
8	chr3:101366400-101390400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:101366400-101392200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr3:101366600-101390800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:101366600-101390800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:101366600-101391000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:101366600-101391000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr3:101366600-101391000	Strong transcription	Fetal Thymus	thymus
15	chr3:101366600-101391800	Strong transcription	Primary B cells from cord blood	blood
16	chr3:101366800-101390400	Strong transcription	Fetal Lung	lung
17	chr3:101366800-101391000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:101366800-101391000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:101367000-101390800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:101367000-101390800	Strong transcription	Dnd41	blood
21	chr3:101367000-101391000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:101367000-101391000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:101367000-101391000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:101367000-101391000	Strong transcription	Placenta	Placenta
25	chr3:101367000-101391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:101367200-101391000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:101367200-101391800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:101367400-101391000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:101367400-101391000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:101367600-101390400	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:101368000-101390600	Strong transcription	Adipose Nuclei	Adipose
32	chr3:101368000-101391000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:101368000-101391600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:101368200-101391000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:101368400-101390400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:101368400-101391000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr3:101369000-101390800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:101369400-101391000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:101369800-101390200	Strong transcription	Fetal Intestine Large	intestine
40	chr3:101369800-101390400	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:101369800-101390600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:101369800-101391000	Strong transcription	Left Ventricle	heart
43	chr3:101370000-101389800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:101371000-101394800	Weak transcription	Small Intestine	intestine
45	chr3:101373000-101390400	Strong transcription	Thymus	Thymus
46	chr3:101373000-101390800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:101373200-101393800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:101373200-101394000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:101374200-101394600	Weak transcription	Esophagus	oesophagus
50	chr3:101380600-101393000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links