Variant report

Variant	rs9988512
Chromosome Location	chr1:61742614-61742615
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:61715305..61718261-chr1:61740987..61743600,2	K562	blood:
2	chr1:61741419..61744047-chr1:61744125..61746996,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11802718	0.89[AFR][1000 genomes]
rs72911904	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72911905	0.95[AFR][1000 genomes]
rs72911907	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72911909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72929861	0.89[AFR][1000 genomes]
rs72929865	0.95[AFR][1000 genomes]
rs72929868	0.95[AFR][1000 genomes]
rs72929875	0.89[AFR][1000 genomes]
rs72929877	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72929880	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9988610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61720800-61755800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:61721000-61754400	Weak transcription	Pancreas	Pancrea
3	chr1:61725800-61750400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:61726000-61742800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:61726000-61743200	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:61729600-61754400	Weak transcription	Lung	lung
7	chr1:61732600-61742800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:61732800-61750000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:61735600-61743200	Weak transcription	Fetal Stomach	stomach
10	chr1:61737000-61750000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:61737200-61751600	Weak transcription	Hela-S3	cervix
12	chr1:61737400-61747600	Weak transcription	HepG2	liver
13	chr1:61737400-61750000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:61737400-61751800	Weak transcription	Esophagus	oesophagus
15	chr1:61737600-61750200	Weak transcription	NHEK	skin
16	chr1:61738000-61752600	Weak transcription	HUVEC	blood vessel
17	chr1:61739000-61746200	Enhancers	Fetal Brain Male	brain
18	chr1:61739200-61742800	Weak transcription	Left Ventricle	heart
19	chr1:61739400-61745400	Weak transcription	Small Intestine	intestine
20	chr1:61739800-61742800	Weak transcription	Psoas Muscle	Psoas
21	chr1:61740800-61748000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:61741000-61742800	Weak transcription	Aorta	Aorta
23	chr1:61741000-61742800	Enhancers	Fetal Lung	lung
24	chr1:61741000-61743000	Weak transcription	Right Atrium	heart
25	chr1:61741000-61747600	Weak transcription	Liver	Liver
26	chr1:61741200-61742800	Weak transcription	Fetal Brain Female	brain
27	chr1:61741800-61742800	Enhancers	Brain Germinal Matrix	brain
28	chr1:61741800-61742800	Enhancers	Rectal Smooth Muscle	rectum
29	chr1:61741800-61742800	Enhancers	A549	lung
30	chr1:61741800-61743000	Enhancers	Brain Angular Gyrus	brain
31	chr1:61741800-61746000	Enhancers	Colon Smooth Muscle	Colon
32	chr1:61742000-61743000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr1:61742000-61743200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr1:61742000-61743200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:61742000-61743200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:61742000-61743800	Enhancers	Fetal Heart	heart
37	chr1:61742200-61742800	Enhancers	Adipose Nuclei	Adipose
38	chr1:61742200-61742800	Weak transcription	Brain Anterior Caudate	brain
39	chr1:61742200-61742800	Weak transcription	Brain Substantia Nigra	brain
40	chr1:61742200-61745200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:61742400-61742800	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:61742400-61743400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr1:61742400-61744800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:61742600-61742800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:61742600-61742800	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr1:61742600-61742800	Active TSS	NHDF-Ad	bronchial
47	chr1:61742600-61743000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:61742600-61743000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr1:61742600-61743200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:61742600-61743200	Flanking Active TSS	Stomach Smooth Muscle	stomach

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