Variant report

Variant	rs10489910
Chromosome Location	chr1:61846933-61846934
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:61842507..61844898-chr1:61846678..61850358,3	K562	blood:
2	chr1:61845747..61850628-chr1:61851992..61855233,6	K562	blood:
3	chr1:61845747..61848557-chr1:61853337..61855233,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17265650	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17265671	0.90[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2067774	1.00[CHB][hapmap]
rs2364479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58054723	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6675218	1.00[CHB][hapmap]
rs72666653	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72666658	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72666659	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72666660	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72666663	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72666667	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74086944	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7533561	0.90[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7545732	0.91[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7555828	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61804400-61851400	Weak transcription	Small Intestine	intestine
2	chr1:61804400-61854600	Weak transcription	Placenta	Placenta
3	chr1:61805800-61848800	Weak transcription	Pancreas	Pancrea
4	chr1:61814000-61848800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:61814600-61848800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:61819000-61848800	Weak transcription	Lung	lung
7	chr1:61820600-61848800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:61823400-61854800	Weak transcription	Spleen	Spleen
9	chr1:61825200-61847200	Weak transcription	A549	lung
10	chr1:61825200-61848600	Weak transcription	Hela-S3	cervix
11	chr1:61825200-61849000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:61825200-61849000	Weak transcription	Ovary	ovary
13	chr1:61825600-61848800	Weak transcription	Gastric	stomach
14	chr1:61826200-61851600	Weak transcription	Fetal Intestine Small	intestine
15	chr1:61826400-61848800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:61827000-61848600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:61827000-61849000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:61828200-61848800	Weak transcription	Fetal Intestine Large	intestine
19	chr1:61828200-61854600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:61828600-61848800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:61833400-61848800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:61833400-61849000	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:61834400-61849000	Weak transcription	Brain Anterior Caudate	brain
24	chr1:61834800-61852000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:61836600-61848800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:61836800-61848600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:61836800-61848800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:61836800-61852200	Weak transcription	Esophagus	oesophagus
29	chr1:61837400-61848600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:61838600-61847200	Weak transcription	HUVEC	blood vessel
31	chr1:61838800-61849000	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:61839600-61854400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:61841400-61849200	Weak transcription	Fetal Brain Male	brain
34	chr1:61841400-61858200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:61841600-61848600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:61841600-61848800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:61841600-61848800	Weak transcription	Brain Substantia Nigra	brain
38	chr1:61841600-61848800	Weak transcription	Fetal Stomach	stomach
39	chr1:61841600-61849000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:61841600-61849000	Weak transcription	Fetal Lung	lung
41	chr1:61841600-61852200	Weak transcription	Right Atrium	heart
42	chr1:61841600-61854800	Weak transcription	HMEC	breast
43	chr1:61841600-61855600	Weak transcription	NHEK	skin
44	chr1:61841800-61848600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:61841800-61848800	Weak transcription	Aorta	Aorta
46	chr1:61841800-61849000	Weak transcription	Fetal Brain Female	brain
47	chr1:61841800-61854400	Weak transcription	Right Ventricle	heart
48	chr1:61843800-61855800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:61844400-61848600	Weak transcription	Liver	Liver
50	chr1:61844400-61848800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links