Variant report

Variant	rs236308
Chromosome Location	chr1:94086524-94086525
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94085180..94089812-chr1:94310226..94315311,7	MCF-7	breast:
2	chr1:94078919..94081222-chr1:94084993..94086695,2	K562	blood:
3	chr1:94084156..94086845-chr1:94089262..94091205,3	K562	blood:
4	chr1:94085637..94087323-chr1:94315969..94317684,2	MCF-7	breast:
5	chr1:94053174..94055459-chr1:94085233..94086891,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000211575	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12084853	0.90[JPT][hapmap]
rs12568405	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1292929	0.81[AMR][1000 genomes]
rs1772781	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1772782	0.84[ASN][1000 genomes]
rs236266	0.90[JPT][hapmap]
rs236267	0.80[ASN][1000 genomes]
rs236273	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs236277	0.80[ASN][1000 genomes]
rs236284	0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs236285	0.85[AMR][1000 genomes]
rs236287	0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs236288	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs236291	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs236295	0.90[JPT][hapmap]
rs236296	0.89[JPT][hapmap]
rs236301	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs236306	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236307	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236311	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs236312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs236313	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs236343	0.87[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes]
rs236344	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs236345	0.88[EUR][1000 genomes]
rs368888	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3767979	0.88[CHB][hapmap]
rs3767981	0.80[ASN][1000 genomes]
rs3767987	0.80[ASN][1000 genomes]
rs3767991	0.90[JPT][hapmap]
rs399649	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs423493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541387	0.90[JPT][hapmap]
rs6702036	0.90[JPT][hapmap]
rs6704479	0.88[JPT][hapmap]
rs798213	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs798217	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs798218	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94077200-94099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:94079400-94086800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:94079400-94088600	Enhancers	Fetal Intestine Large	intestine
5	chr1:94079600-94088000	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:94079600-94089400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:94079800-94090000	Enhancers	Stomach Mucosa	stomach
8	chr1:94080000-94088000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:94080000-94089200	Genic enhancers	NHEK	skin
10	chr1:94081200-94095000	Genic enhancers	HSMM	muscle
11	chr1:94082200-94086600	Weak transcription	K562	blood
12	chr1:94082400-94088000	Enhancers	Fetal Intestine Small	intestine
13	chr1:94083000-94086600	Enhancers	Colonic Mucosa	Colon
14	chr1:94083400-94088000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:94083400-94091200	Weak transcription	Aorta	Aorta
16	chr1:94083400-94093800	Weak transcription	Psoas Muscle	Psoas
17	chr1:94083400-94108200	Weak transcription	Esophagus	oesophagus
18	chr1:94083600-94101600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:94083800-94088000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:94083800-94088200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:94083800-94091200	Weak transcription	Ovary	ovary
22	chr1:94083800-94091400	Weak transcription	Fetal Stomach	stomach
23	chr1:94083800-94095000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:94084000-94086600	Enhancers	Duodenum Mucosa	Duodenum
25	chr1:94084000-94087200	Enhancers	Adipose Nuclei	Adipose
26	chr1:94084000-94088000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:94084000-94088000	Weak transcription	Brain Substantia Nigra	brain
28	chr1:94084000-94088000	Weak transcription	Pancreas	Pancrea
29	chr1:94084000-94089400	Genic enhancers	HMEC	breast
30	chr1:94084000-94089800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:94084000-94090800	Weak transcription	Fetal Lung	lung
32	chr1:94084000-94091000	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:94084000-94091400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:94084200-94087600	Weak transcription	HUVEC	blood vessel
35	chr1:94084200-94087800	Weak transcription	Brain Germinal Matrix	brain
36	chr1:94084200-94087800	Enhancers	A549	lung
37	chr1:94084200-94088000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:94084200-94088000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:94084200-94088000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:94084200-94090000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:94084200-94090800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:94084200-94091400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:94084200-94101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:94084400-94087600	Weak transcription	Liver	Liver
45	chr1:94084400-94088000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:94084400-94088000	Weak transcription	Brain Anterior Caudate	brain
47	chr1:94084400-94091400	Enhancers	HepG2	liver
48	chr1:94084600-94091200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:94085000-94086600	Enhancers	NH-A	brain
50	chr1:94085000-94087000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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