Variant report

Variant	rs34491022
Chromosome Location	chr3:177396516-177396517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:177396390-177398716	SK-N-SH	brain:	n/a	n/a
2	GATA2	chr3:177396460-177396821	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:177396417..177398253-chr3:177403984..177405833,2	MCF-7	breast:
2	chr3:177395868..177398215-chr3:177400550..177402752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228561	TF binding region
ENSG00000228561	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10513747	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10513749	0.85[ASN][1000 genomes]
rs10513750	0.83[ASN][1000 genomes]
rs10936953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915692	0.96[ASN][1000 genomes]
rs12487312	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487458	0.82[ASN][1000 genomes]
rs12489304	0.83[ASN][1000 genomes]
rs12489969	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496321	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13059514	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13060224	0.82[ASN][1000 genomes]
rs13060502	0.82[ASN][1000 genomes]
rs13064192	0.83[ASN][1000 genomes]
rs13071785	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074455	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13082519	0.82[ASN][1000 genomes]
rs13097562	0.84[ASN][1000 genomes]
rs13098037	0.84[ASN][1000 genomes]
rs13340118	0.82[ASN][1000 genomes]
rs13340167	0.82[ASN][1000 genomes]
rs13340172	0.82[ASN][1000 genomes]
rs1499809	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1499811	0.86[ASN][1000 genomes]
rs1500048	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17635512	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17635597	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2062499	0.83[ASN][1000 genomes]
rs2062500	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33964414	0.83[ASN][1000 genomes]
rs34066617	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34347103	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34407557	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34557886	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34638059	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34763113	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35110045	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35468531	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35610650	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35652846	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35791913	0.83[ASN][1000 genomes]
rs35830472	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35847814	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35868955	0.83[ASN][1000 genomes]
rs36055300	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56005554	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57405296	0.82[ASN][1000 genomes]
rs61541774	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62283347	0.80[ASN][1000 genomes]
rs66636257	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67189039	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67797381	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6793629	0.82[ASN][1000 genomes]
rs68151580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71308158	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7610506	0.83[ASN][1000 genomes]
rs7639373	0.83[ASN][1000 genomes]
rs7641099	0.82[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	esv2752972	chr3:176924298-177425298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv4131	chr3:177366549-177399301	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2590986	chr3:177395894-177397383	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177383800-177397800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:177391200-177397600	Weak transcription	Right Atrium	heart
3	chr3:177391600-177396800	Weak transcription	Dnd41	blood
4	chr3:177391800-177397600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:177392000-177405400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:177392200-177396800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:177392200-177397200	Weak transcription	HMEC	breast
8	chr3:177392200-177397200	Weak transcription	Osteobl	bone
9	chr3:177392200-177397400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:177392200-177397600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:177392200-177397600	Weak transcription	Adipose Nuclei	Adipose
12	chr3:177392200-177397800	Weak transcription	NHLF	lung
13	chr3:177392200-177404400	Weak transcription	Ovary	ovary
14	chr3:177392400-177396600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:177392400-177397200	Weak transcription	K562	blood
16	chr3:177392400-177397200	Weak transcription	NH-A	brain
17	chr3:177392400-177397400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:177392400-177397600	Weak transcription	NHDF-Ad	bronchial
19	chr3:177392400-177397800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:177392400-177418800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:177392600-177397400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:177392600-177397400	Weak transcription	Fetal Thymus	thymus
23	chr3:177392600-177397600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:177392600-177398600	Weak transcription	Spleen	Spleen
25	chr3:177392600-177399600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:177394000-177401000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:177394800-177404800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:177395000-177396600	Weak transcription	Fetal Heart	heart
29	chr3:177395000-177396800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:177395000-177396800	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:177395000-177397000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:177395000-177406000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:177395000-177411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:177395200-177397000	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr3:177395200-177397400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:177395200-177399600	Weak transcription	Stomach Mucosa	stomach
37	chr3:177395200-177400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:177395400-177399600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:177395400-177400200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:177395600-177397400	Weak transcription	Fetal Lung	lung
41	chr3:177395800-177396600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:177396000-177398600	Enhancers	Primary hematopoietic stem cells	blood
43	chr3:177396000-177401000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr3:177396000-177401200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:177396200-177396600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:177396400-177396600	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:177396400-177397400	Enhancers	HUVEC	blood vessel
48	chr3:177396400-177398200	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links