Variant report

Variant	rs73240314
Chromosome Location	chr3:142255090-142255091
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	chr3:142165873..142168025-chr3:142253453..142255156,2	MCF-7	breast:
2	chr3:142229095..142231741-chr3:142253840..142256348,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114127	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10935464	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2229032	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28365824	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3922731	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55994893	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56397702	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60001529	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66597875	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228757	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73228758	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73238195	0.86[EUR][1000 genomes]
rs73238200	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73238201	0.85[ASN][1000 genomes]
rs73238202	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73240305	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73240309	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73240310	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73240316	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73240318	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73240323	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73240328	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9858204	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
3	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142203000-142255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:142203800-142255200	Weak transcription	Gastric	stomach
6	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
7	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
8	chr3:142209400-142271800	Weak transcription	HepG2	liver
9	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
10	chr3:142231600-142255200	Weak transcription	Aorta	Aorta
11	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
12	chr3:142233600-142255200	Weak transcription	Fetal Stomach	stomach
13	chr3:142233600-142271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:142238600-142269000	Weak transcription	Fetal Intestine Small	intestine
15	chr3:142239800-142269600	Weak transcription	Thymus	Thymus
16	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
17	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:142241800-142270800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:142242400-142275800	Weak transcription	NHEK	skin
20	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
21	chr3:142248200-142258400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:142248400-142269000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:142248600-142273600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:142249400-142255600	Strong transcription	A549	lung
26	chr3:142249400-142257200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:142249400-142257600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:142249400-142258200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:142249600-142255600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr3:142249800-142257000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:142250400-142261600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:142250800-142255400	Strong transcription	Liver	Liver
33	chr3:142250800-142255600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:142250800-142255600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:142250800-142256200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr3:142251000-142255400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:142251000-142255600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:142251000-142255600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:142251000-142255600	Strong transcription	Brain Hippocampus Middle	brain
40	chr3:142251000-142256000	Strong transcription	Primary T cells from cord blood	blood
41	chr3:142251000-142256200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:142251000-142256200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:142251000-142256200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:142251000-142256200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:142251000-142256200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:142251000-142256400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:142251000-142256400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr3:142251000-142257000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:142251000-142257200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:142251000-142257400	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links