Variant report

Variant	rs3010292
Chromosome Location	chr6:139802995-139802996
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139693137..139696900-chr6:139799148..139803009,4	K562	blood:
2	chr6:139795946..139798274-chr6:139802764..139804469,2	MCF-7	breast:
3	chr6:139797780..139800668-chr6:139802147..139805671,5	K562	blood:
4	chr6:139801890..139804566-chr6:139874665..139876366,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1159968	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2908508	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3010289	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3010290	0.81[ASN][1000 genomes]
rs3010291	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3010293	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3010294	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010295	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3010296	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3010298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139796800-139806600	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:139797000-139806800	Weak transcription	Fetal Lung	lung
3	chr6:139797200-139803200	Weak transcription	Fetal Kidney	kidney
4	chr6:139797600-139803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:139797800-139803000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:139800200-139804000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:139800200-139804400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:139800400-139804400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:139800600-139804600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:139800600-139805200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:139800800-139804400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:139800800-139805200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:139800800-139805200	Enhancers	Liver	Liver
14	chr6:139801000-139803600	Weak transcription	Fetal Stomach	stomach
15	chr6:139801000-139804600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:139801600-139803200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:139801600-139803400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:139802200-139803000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:139802200-139803400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:139802200-139803400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:139802200-139803400	Weak transcription	K562	blood
22	chr6:139802200-139803600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:139802400-139803000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:139802400-139804000	Enhancers	HepG2	liver
25	chr6:139802400-139807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:139802600-139804600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:139802800-139804000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:139802800-139804200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links