Variant report

Variant	rs61859001
Chromosome Location	chr10:43926491-43926492
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43914969..43916582-chr10:43923681..43926679,2	MCF-7	breast:
2	chr10:43923300..43926779-chr10:43929702..43934389,5	K562	blood:
3	chr10:43919994..43922298-chr10:43925539..43927816,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF487P-3	chr10:43926290-43927317	NONHSAT012965

Variant related genes	Relation type
ENSG00000230555	Chromatin interaction
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11238518	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11238519	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11238520	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11238531	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238533	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238547	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238570	1.00[ASN][1000 genomes]
rs11238591	1.00[ASN][1000 genomes]
rs11238605	1.00[ASN][1000 genomes]
rs12263722	1.00[ASN][1000 genomes]
rs12354765	0.87[AMR][1000 genomes]
rs12356024	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356570	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359520	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359825	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359980	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154006	1.00[ASN][1000 genomes]
rs17154012	1.00[ASN][1000 genomes]
rs17154020	1.00[ASN][1000 genomes]
rs17366560	1.00[ASN][1000 genomes]
rs17447133	1.00[ASN][1000 genomes]
rs17447468	1.00[ASN][1000 genomes]
rs17447580	1.00[ASN][1000 genomes]
rs41313824	1.00[ASN][1000 genomes]
rs4646975	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948720	1.00[ASN][1000 genomes]
rs56120769	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57740712	1.00[ASN][1000 genomes]
rs59220072	1.00[ASN][1000 genomes]
rs60163354	1.00[ASN][1000 genomes]
rs61845680	1.00[ASN][1000 genomes]
rs61845682	1.00[ASN][1000 genomes]
rs61858993	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858994	0.84[AMR][1000 genomes]
rs61858995	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61859177	1.00[ASN][1000 genomes]
rs61859178	1.00[ASN][1000 genomes]
rs61859179	1.00[ASN][1000 genomes]
rs61859180	1.00[ASN][1000 genomes]
rs61859181	1.00[ASN][1000 genomes]
rs61859182	1.00[ASN][1000 genomes]
rs61859185	1.00[ASN][1000 genomes]
rs61859441	1.00[ASN][1000 genomes]
rs61859445	1.00[ASN][1000 genomes]
rs61859998	1.00[ASN][1000 genomes]
rs61860007	1.00[ASN][1000 genomes]
rs61860889	1.00[ASN][1000 genomes]
rs67284218	1.00[ASN][1000 genomes]
rs7073767	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079012	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7084706	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093434	1.00[ASN][1000 genomes]
rs7100846	1.00[ASN][1000 genomes]
rs7900284	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7903467	1.00[ASN][1000 genomes]
rs7905073	1.00[ASN][1000 genomes]
rs7906169	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7906484	1.00[ASN][1000 genomes]
rs7913352	1.00[ASN][1000 genomes]
rs7916345	1.00[ASN][1000 genomes]
rs7920408	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription 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	63 gene(s)	inside rSNPs	diseases
7	esv3448813	chr10:43919995-43950867	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43916800-43931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr10:43916800-43931600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr10:43916800-43931600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:43917000-43931600	Weak transcription	Fetal Brain Female	brain
5	chr10:43917200-43930800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:43917200-43930800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:43917200-43931600	Weak transcription	Brain Anterior Caudate	brain
8	chr10:43917400-43930400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:43917400-43930800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:43917400-43930800	Weak transcription	Brain Hippocampus Middle	brain
11	chr10:43917400-43930800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr10:43917400-43930800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:43917400-43931600	Weak transcription	Brain Angular Gyrus	brain
14	chr10:43917600-43930800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr10:43917600-43930800	Weak transcription	Fetal Muscle Leg	muscle
16	chr10:43917600-43931600	Weak transcription	Right Ventricle	heart
17	chr10:43918000-43928000	Weak transcription	Fetal Intestine Small	intestine
18	chr10:43920000-43930400	Weak transcription	Liver	Liver
19	chr10:43920000-43930400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr10:43920200-43931600	Weak transcription	Fetal Lung	lung
21	chr10:43921800-43926600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr10:43921800-43931200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr10:43922800-43930400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr10:43922800-43930600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr10:43923400-43930400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:43923400-43931000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:43923600-43927000	Weak transcription	Primary B cells from cord blood	blood
28	chr10:43923600-43928800	Weak transcription	Fetal Stomach	stomach
29	chr10:43923600-43931400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr10:43923800-43930400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr10:43923800-43931600	Weak transcription	Primary T cells from cord blood	blood
32	chr10:43924600-43930600	Weak transcription	Fetal Intestine Large	intestine
33	chr10:43925200-43927600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr10:43925800-43931600	Weak transcription	Left Ventricle	heart
35	chr10:43926000-43931000	Weak transcription	Adipose Nuclei	Adipose
36	chr10:43926000-43931000	Weak transcription	Placenta	Placenta
37	chr10:43926400-43927200	Enhancers	K562	blood
38	chr10:43926400-43931400	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links