Variant report

Variant	rs12304179
Chromosome Location	chr12:122049566-122049567
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122048372..122050638-chr12:122068464..122071383,2	K562	blood:
2	chr12:122017331..122020300-chr12:122047216..122050900,4	K562	blood:
3	chr12:122042259..122044825-chr12:122047576..122049866,3	K562	blood:

Variant related genes	Relation type
ENSG00000252393	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000256742	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10770183	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840610	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10840648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10840650	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10840651	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11043181	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11043296	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11043306	0.88[ASN][1000 genomes]
rs11043308	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11043316	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11614109	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12305333	0.86[AMR][1000 genomes]
rs12315280	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319633	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12322922	0.81[ASN][1000 genomes]
rs1983269	0.83[ASN][1000 genomes]
rs28435255	0.85[EUR][1000 genomes]
rs28489288	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28552516	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28594507	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35806699	0.83[ASN][1000 genomes]
rs7484839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7485243	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7487117	0.85[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	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122028800-122064000	Weak transcription	Right Atrium	heart
2	chr12:122029200-122049800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:122033200-122049600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:122033800-122049600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:122047400-122049600	Enhancers	Placenta	Placenta
6	chr12:122047600-122049600	Enhancers	Fetal Muscle Trunk	muscle
7	chr12:122047600-122050000	Enhancers	Fetal Stomach	stomach
8	chr12:122048000-122049600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr12:122048000-122049600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr12:122048000-122049800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:122048000-122050000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:122048000-122050000	Enhancers	Fetal Muscle Leg	muscle
13	chr12:122048200-122049800	Enhancers	Fetal Brain Male	brain
14	chr12:122048200-122050000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:122048400-122049800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:122048400-122050000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr12:122048400-122050000	Enhancers	Brain Anterior Caudate	brain
18	chr12:122048400-122050200	Enhancers	Rectal Smooth Muscle	rectum
19	chr12:122048400-122050200	Enhancers	K562	blood
20	chr12:122048600-122049800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:122048600-122050200	Enhancers	Colon Smooth Muscle	Colon
22	chr12:122048800-122049600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:122048800-122049600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:122048800-122049600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:122048800-122051400	Weak transcription	Adipose Nuclei	Adipose
26	chr12:122048800-122062800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:122048800-122062800	Weak transcription	Fetal Intestine Small	intestine
28	chr12:122049000-122049800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:122049000-122049800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:122049000-122050000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:122049000-122053000	Weak transcription	HepG2	liver
32	chr12:122049200-122049600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:122049200-122049600	Enhancers	Esophagus	oesophagus
34	chr12:122049200-122049600	Enhancers	Psoas Muscle	Psoas
35	chr12:122049200-122049600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr12:122049200-122049800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr12:122049200-122049800	Enhancers	Lung	lung
38	chr12:122049200-122049800	Enhancers	Hela-S3	cervix
39	chr12:122049400-122049600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:122049400-122050000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:122049400-122051200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:122049400-122062800	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links