Variant report

Variant	rs2961573
Chromosome Location	chr10:4871215-4871216
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:4861761..4864684-chr10:4870409..4873110,2	K562	blood:
2	chr10:4868628..4871525-chr10:4902310..4904323,2	K562	blood:
3	chr10:4869791..4871610-chr10:4890458..4893097,2	K562	blood:
4	chr10:4869493..4871695-chr10:5409479..5411082,2	K562	blood:
5	chr10:4866089..4871671-chr10:4873094..4876081,6	MCF-7	breast:
6	chr10:4869313..4873235-chr10:4874956..4878368,5	K562	blood:
7	chr10:4867480..4871698-chr10:4879074..4886734,7	K562	blood:
8	chr10:4869756..4872068-chr10:4996333..4999086,2	MCF-7	breast:
9	chr10:4869978..4871994-chr10:5334140..5336719,2	K562	blood:
10	chr10:4869420..4871876-chr10:5136948..5139293,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196139	Chromatin interaction
ENSG00000165568	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10751991	0.84[EUR][1000 genomes]
rs10795205	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10904366	0.84[EUR][1000 genomes]
rs1901645	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924269	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924271	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924273	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924276	1.00[ASN][1000 genomes]
rs2924278	0.82[ASN][1000 genomes]
rs2961561	1.00[ASN][1000 genomes]
rs2961562	1.00[ASN][1000 genomes]
rs2961564	1.00[ASN][1000 genomes]
rs2961569	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961570	0.98[AFR][1000 genomes]
rs2961572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961574	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961577	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961580	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961582	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961583	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961584	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961585	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961597	0.81[AMR][1000 genomes]
rs3924660	0.81[EUR][1000 genomes]
rs4242772	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242773	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242774	0.84[EUR][1000 genomes]
rs4242780	0.84[EUR][1000 genomes]
rs4317889	0.81[EUR][1000 genomes]
rs4347286	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465268	0.81[EUR][1000 genomes]
rs4562702	0.84[EUR][1000 genomes]
rs4578280	0.84[EUR][1000 genomes]
rs4626979	0.88[EUR][1000 genomes]
rs4881356	0.81[AMR][1000 genomes]
rs4881369	0.81[EUR][1000 genomes]
rs6601866	0.84[EUR][1000 genomes]
rs7077134	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4868800-4874600	Weak transcription	Spleen	Spleen
2	chr10:4868800-4879800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:4869000-4875000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr10:4869000-4881000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:4869200-4872800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:4869200-4873400	Weak transcription	Fetal Stomach	stomach
7	chr10:4869200-4874000	Weak transcription	Lung	lung
8	chr10:4869200-4875400	Weak transcription	Ovary	ovary
9	chr10:4869200-4875600	Weak transcription	Gastric	stomach
10	chr10:4869200-4876600	Weak transcription	Fetal Brain Female	brain
11	chr10:4869200-4877600	Weak transcription	Pancreas	Pancrea
12	chr10:4869200-4877800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:4869200-4883600	Weak transcription	Thymus	Thymus
14	chr10:4869200-4884800	Weak transcription	Esophagus	oesophagus
15	chr10:4869200-4889200	Weak transcription	NHLF	lung
16	chr10:4869200-4889600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:4869200-4890400	Weak transcription	Right Atrium	heart
18	chr10:4869200-4891600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr10:4869200-4892200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:4869400-4873000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:4869400-4873000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr10:4869400-4873000	Weak transcription	Fetal Muscle Leg	muscle
23	chr10:4869400-4873000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr10:4869400-4873200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:4869400-4873400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr10:4869400-4876000	Weak transcription	Brain Germinal Matrix	brain
27	chr10:4869400-4877200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:4869400-4877600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr10:4869400-4878400	Weak transcription	Placenta	Placenta
30	chr10:4869400-4879000	Weak transcription	Fetal Lung	lung
31	chr10:4869400-4883400	Weak transcription	Colonic Mucosa	Colon
32	chr10:4869400-4886800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:4869400-4889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:4869400-4889600	Weak transcription	HSMM	muscle
35	chr10:4869400-4891600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr10:4869600-4872400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:4869600-4872800	Weak transcription	Aorta	Aorta
38	chr10:4869600-4872800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr10:4869600-4873000	Weak transcription	Adipose Nuclei	Adipose
40	chr10:4869600-4873000	Weak transcription	Fetal Kidney	kidney
41	chr10:4869600-4873200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:4869600-4875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:4869600-4875600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:4869600-4877000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr10:4869600-4877200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr10:4869600-4877200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:4869600-4877600	Weak transcription	Osteobl	bone
48	chr10:4869600-4878600	Weak transcription	Colon Smooth Muscle	Colon
49	chr10:4869600-4883400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr10:4869600-4885000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links