Variant report

Variant	rs16845230
Chromosome Location	chr1:225939199-225939200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225936802..225939434-chr1:225952495..225954139,2	MCF-7	breast:
2	chr1:225938850..225941091-chr1:225955099..225957514,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRP9-1	chr1:225939022-225939945	ENSG00000227496.1

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16845207	0.85[EUR][1000 genomes]
rs16845221	0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs16845250	0.85[EUR][1000 genomes]
rs2077840	0.85[EUR][1000 genomes]
rs56052403	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74148699	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225934800-225939400	Weak transcription	Fetal Brain Female	brain
2	chr1:225934800-225943200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:225935000-225941000	Weak transcription	Hela-S3	cervix
4	chr1:225935000-225949600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:225935200-225942800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:225935600-225939200	Weak transcription	Stomach Mucosa	stomach
7	chr1:225935600-225941000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:225935600-225942600	Weak transcription	Fetal Thymus	thymus
9	chr1:225935600-225942600	Weak transcription	Pancreas	Pancrea
10	chr1:225935800-225942800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:225936000-225939600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:225936000-225939600	Weak transcription	Fetal Brain Male	brain
13	chr1:225936000-225942800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:225936000-225942800	Weak transcription	A549	lung
15	chr1:225936200-225943400	Weak transcription	Esophagus	oesophagus
16	chr1:225937600-225939200	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr1:225937600-225939200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:225937600-225939800	Enhancers	Fetal Muscle Leg	muscle
19	chr1:225937600-225940000	Enhancers	Stomach Smooth Muscle	stomach
20	chr1:225937600-225940200	Enhancers	Fetal Lung	lung
21	chr1:225937800-225939200	Enhancers	Fetal Stomach	stomach
22	chr1:225938000-225939200	Enhancers	Right Atrium	heart
23	chr1:225938000-225939400	Enhancers	HSMM	muscle
24	chr1:225938000-225939600	Enhancers	Fetal Muscle Trunk	muscle
25	chr1:225938000-225939600	Enhancers	Right Ventricle	heart
26	chr1:225938000-225939800	Enhancers	Left Ventricle	heart
27	chr1:225938000-225939800	Enhancers	Ovary	ovary
28	chr1:225938000-225939800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:225938000-225941000	Enhancers	Placenta	Placenta
30	chr1:225938200-225939200	Enhancers	HSMMtube	muscle
31	chr1:225938200-225939600	Enhancers	Psoas Muscle	Psoas
32	chr1:225938400-225939800	Weak transcription	HepG2	liver
33	chr1:225938400-225942600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:225938600-225939200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:225938600-225939200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:225938600-225942600	Weak transcription	Lung	lung
37	chr1:225938600-225945200	Weak transcription	Small Intestine	intestine
38	chr1:225938800-225939200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:225938800-225939400	Enhancers	Fetal Kidney	kidney
40	chr1:225938800-225939600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:225938800-225939800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:225938800-225940000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:225938800-225940200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:225938800-225940200	Enhancers	Brain Germinal Matrix	brain
45	chr1:225938800-225942800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:225938800-225943200	Weak transcription	Gastric	stomach
47	chr1:225939000-225939400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:225939000-225939800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr1:225939000-225939800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr1:225939000-225942600	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links