Variant report

Variant	rs1701699
Chromosome Location	chr12:56296347-56296348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56224247..56225882-chr12:56295667..56297229,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182796	Chromatin interaction
ENSG00000135392	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10128982	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1052206	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747760	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10783774	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783775	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876858	0.86[ASN][1000 genomes]
rs10876861	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876862	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171688	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1136082	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12298127	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12320309	0.87[ASN][1000 genomes]
rs1681070	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1681082	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1701698	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1807168	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2101718	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4414258	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61956428	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581086	0.84[ASN][1000 genomes]
rs6581087	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs705711	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705715	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7135133	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7297871	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7308505	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7312870	0.82[EUR][1000 genomes]
rs772461	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs772462	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs772468	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs772473	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs772475	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs772700	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7979046	0.87[ASN][1000 genomes]
rs9739192	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739196	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	esv3347258	chr12:56267734-56298106	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56279800-56320000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56285200-56320000	Weak transcription	Pancreas	Pancrea
3	chr12:56291000-56308400	Weak transcription	Right Atrium	heart
4	chr12:56291400-56296800	Weak transcription	HUVEC	blood vessel
5	chr12:56291400-56319000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:56292000-56298600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:56292600-56298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:56292800-56296800	Weak transcription	Colonic Mucosa	Colon
9	chr12:56292800-56297200	Strong transcription	Fetal Brain Female	brain
10	chr12:56292800-56297600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:56292800-56297600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:56292800-56297600	Strong transcription	Primary B cells from cord blood	blood
13	chr12:56292800-56297600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:56292800-56297800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:56292800-56298000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:56292800-56316000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:56293000-56297200	Strong transcription	Placenta	Placenta
18	chr12:56293000-56298000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:56293000-56307800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:56293200-56296600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:56293200-56296800	Weak transcription	NH-A	brain
22	chr12:56293200-56299800	Weak transcription	HSMMtube	muscle
23	chr12:56293200-56307000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:56293200-56307200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:56293200-56307400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:56293400-56296800	Weak transcription	HSMM	muscle
27	chr12:56293400-56297000	Weak transcription	HMEC	breast
28	chr12:56293400-56300000	Weak transcription	A549	lung
29	chr12:56293600-56297400	Strong transcription	Fetal Muscle Leg	muscle
30	chr12:56293600-56319200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:56293800-56297600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:56293800-56319600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:56294000-56297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:56294000-56297200	Strong transcription	Brain Germinal Matrix	brain
35	chr12:56294000-56297400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:56294000-56297400	Strong transcription	Adipose Nuclei	Adipose
37	chr12:56294000-56297400	Strong transcription	Fetal Intestine Small	intestine
38	chr12:56294000-56297600	Strong transcription	Liver	Liver
39	chr12:56294000-56297600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:56294000-56297600	Strong transcription	Fetal Thymus	thymus
41	chr12:56294000-56298000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:56294000-56298000	Strong transcription	Fetal Stomach	stomach
43	chr12:56294200-56296800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:56294200-56297200	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr12:56294200-56297200	Strong transcription	Primary T cells from cord blood	blood
46	chr12:56294200-56297200	Strong transcription	Lung	lung
47	chr12:56294200-56297400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:56294200-56297400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:56294200-56297400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:56294200-56297400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links