Variant report

Variant	rs61785598
Chromosome Location	chr1:9961538-9961539
allele	A/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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9960502..9962107-chr1:9968880..9970724,2	MCF-7	breast:
2	chr1:9960360..9963162-chr1:10094643..10096453,2	K562	blood:
3	chr1:9959637..9962157-chr1:10000997..10004745,4	K562	blood:
4	chr1:9959497..9963763-chr1:9965322..9971774,8	K562	blood:
5	chr1:9958976..9964207-chr1:9967620..9971774,11	K562	blood:
6	chr1:9958455..9962584-chr1:9963252..9967560,5	MCF-7	breast:
7	chr1:9943285..9945360-chr1:9959805..9962322,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMNAT1-2	chr1:9961518-9961630	ENSG00000234374.1

No data

Variant related genes	Relation type
ENSG00000228150	Chromatin interaction
ENSG00000178585	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11808614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57237552	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61785591	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61785593	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6541067	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6659441	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6686017	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690524	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74054125	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74054138	0.83[AMR][1000 genomes]
rs7529783	0.83[AMR][1000 genomes]
rs7536748	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7537879	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7554923	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9943200-9961600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:9949400-9967600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:9951200-9961600	Weak transcription	Fetal Brain Female	brain
4	chr1:9951400-9962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:9951600-9961800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:9951600-9969000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:9954000-9964600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:9954600-9961600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:9958000-9968800	Weak transcription	Fetal Stomach	stomach
10	chr1:9958800-9969000	Weak transcription	Hela-S3	cervix
11	chr1:9959000-9964400	Weak transcription	HSMMtube	muscle
12	chr1:9959000-9964400	Weak transcription	NH-A	brain
13	chr1:9959000-9964800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:9959600-9963800	Enhancers	Stomach Mucosa	stomach
15	chr1:9959800-9962800	Enhancers	Lung	lung
16	chr1:9960000-9961800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:9960000-9962400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:9960000-9962600	Enhancers	Fetal Lung	lung
19	chr1:9960000-9962800	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:9960200-9961600	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:9960200-9962200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:9960200-9962400	Enhancers	Esophagus	oesophagus
23	chr1:9960200-9962400	Genic enhancers	Fetal Intestine Small	intestine
24	chr1:9960200-9962400	Enhancers	Fetal Thymus	thymus
25	chr1:9960200-9962600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:9960200-9962800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:9960400-9962200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:9960400-9962400	Enhancers	K562	blood
29	chr1:9960400-9962800	Enhancers	Ovary	ovary
30	chr1:9960400-9962800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:9960600-9961600	Flanking Active TSS	Fetal Heart	heart
32	chr1:9960600-9962000	Enhancers	Brain Germinal Matrix	brain
33	chr1:9960600-9962000	Enhancers	HMEC	breast
34	chr1:9960600-9962400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:9960600-9962400	Enhancers	Psoas Muscle	Psoas
36	chr1:9960600-9962600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:9960600-9962800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:9960600-9962800	Enhancers	Fetal Muscle Leg	muscle
39	chr1:9960800-9961800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr1:9960800-9961800	Enhancers	HSMM	muscle
41	chr1:9960800-9962400	Enhancers	Fetal Intestine Large	intestine
42	chr1:9960800-9962600	Enhancers	Brain Angular Gyrus	brain
43	chr1:9960800-9967800	Weak transcription	Thymus	Thymus
44	chr1:9960800-9969400	Weak transcription	Aorta	Aorta
45	chr1:9961000-9961600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:9961000-9961600	Enhancers	Primary B cells from peripheral blood	blood
47	chr1:9961000-9961600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr1:9961000-9961800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:9961000-9961800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:9961000-9961800	Enhancers	Primary neutrophils fromperipheralblood	blood

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