Variant report

Variant	rs12096283
Chromosome Location	chr1:10459958-10459959
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10457879..10460190-chr8:103875742..103877594,2	MCF-7	breast:
2	chr1:10457490..10461716-chr1:10469511..10473951,6	K562	blood:
3	chr1:10447111..10452516-chr1:10455817..10460024,9	K562	blood:
4	chr1:10457843..10460253-chr1:10533493..10537083,3	MCF-7	breast:
5	chr1:10446399..10450088-chr1:10457513..10461303,7	MCF-7	breast:
6	chr1:10457403..10461622-chr1:10531171..10536559,7	K562	blood:
7	chr1:10269636..10272138-chr1:10457591..10460138,4	K562	blood:
8	chr1:10457797..10461098-chr1:10474071..10478087,9	K562	blood:
9	chr1:10446950..10451985-chr1:10457311..10462205,6	K562	blood:
10	chr1:9882661..9885013-chr1:10458252..10460185,2	K562	blood:
11	chr1:10269508..10272201-chr1:10459062..10462119,3	K562	blood:
12	chr1:10446221..10450110-chr1:10457451..10462205,13	MCF-7	breast:
13	chr1:10001846..10004168-chr1:10458912..10460649,2	K562	blood:
14	chr1:10457794..10460664-chr1:10487844..10492697,5	K562	blood:
15	chr1:10457794..10461321-chr1:10487053..10491931,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000175279	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000265945	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000054523	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000271989	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11121540	0.95[AFR][1000 genomes]
rs11121558	0.95[AFR][1000 genomes]
rs11799743	1.00[MEX][hapmap]
rs17034738	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6669115	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
7	nsv8213	chr1:10450914-10460439	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10458000-10460200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:10458000-10460200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:10458200-10460000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:10458200-10460000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:10458200-10460000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:10458200-10460000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:10458200-10460000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:10458200-10460000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:10458200-10460000	Active TSS	Esophagus	oesophagus
10	chr1:10458200-10460000	Active TSS	Fetal Kidney	kidney
11	chr1:10458200-10460000	Active TSS	Fetal Lung	lung
12	chr1:10458200-10460000	Active TSS	Ovary	ovary
13	chr1:10458200-10460000	Active TSS	Psoas Muscle	Psoas
14	chr1:10458200-10460000	Active TSS	Hela-S3	cervix
15	chr1:10458200-10460000	Active TSS	K562	blood
16	chr1:10458200-10460000	Active TSS	Osteobl	bone
17	chr1:10458200-10460200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr1:10458200-10460200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr1:10458200-10460200	Active TSS	H1 Cell Line	embryonic stem cell
20	chr1:10458200-10460200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:10458200-10460200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:10458200-10460200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr1:10458200-10460200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:10458200-10460200	Active TSS	Fetal Muscle Trunk	muscle
25	chr1:10458200-10460200	Active TSS	NHLF	lung
26	chr1:10458200-10460400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:10458200-10460400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:10458200-10460400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr1:10458200-10460800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:10458200-10460800	Active TSS	HSMMtube	muscle
31	chr1:10458400-10460000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:10458400-10460000	Active TSS	Aorta	Aorta
33	chr1:10458400-10460000	Active TSS	Brain Cingulate Gyrus	brain
34	chr1:10458400-10460000	Active TSS	Brain Germinal Matrix	brain
35	chr1:10458400-10460000	Active TSS	Brain Hippocampus Middle	brain
36	chr1:10458400-10460000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:10458400-10460000	Active TSS	Gastric	stomach
38	chr1:10458400-10460000	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:10458400-10460000	Active TSS	Small Intestine	intestine
40	chr1:10458400-10460200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:10458400-10460200	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr1:10458400-10460200	Active TSS	HepG2	liver
43	chr1:10458400-10460200	Active TSS	NHDF-Ad	bronchial
44	chr1:10458400-10460600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr1:10458600-10460000	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr1:10458600-10460000	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr1:10458600-10460200	Active TSS	Stomach Mucosa	stomach
48	chr1:10458600-10460800	Active TSS	HSMM	muscle
49	chr1:10458600-10461000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:10458800-10460000	Active TSS	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links