Variant report

Variant	rs2908508
Chromosome Location	chr6:139800892-139800893
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:139693137..139696900-chr6:139799148..139803009,4	K562	blood:
2	chr6:139797675..139799727-chr6:139800146..139801985,2	K562	blood:
3	chr6:139799364..139800954-chr6:139840362..139842649,2	K562	blood:
4	chr6:139794045..139795703-chr6:139798060..139801025,2	MCF-7	breast:
5	chr6:139694833..139697691-chr6:139800681..139802869,2	K562	blood:
6	chr6:139793599..139796116-chr6:139799932..139801605,2	K562	blood:
7	chr6:139799661..139802615-chr6:139804179..139806515,2	MCF-7	breast:
8	chr6:139799627..139801775-chr6:140085865..140087472,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction
ENSG00000238099	Chromatin interaction

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

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

rs_ID	r²[population]
rs1159968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908496	0.81[JPT][hapmap]
rs3010289	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3010291	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3010292	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]
rs3010293	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010294	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3010295	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3010296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010298	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[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	nsv518835	chr6:139770067-139800892	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	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	chr6:139796800-139801000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:139796800-139806600	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:139797000-139806800	Weak transcription	Fetal Lung	lung
4	chr6:139797200-139803200	Weak transcription	Fetal Kidney	kidney
5	chr6:139797600-139803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:139797800-139803000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:139798000-139801200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:139798800-139801000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:139800200-139802400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:139800200-139804000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:139800200-139804400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:139800400-139801000	Enhancers	Fetal Stomach	stomach
13	chr6:139800400-139801400	Enhancers	K562	blood
14	chr6:139800400-139804400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:139800600-139802000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr6:139800600-139802200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:139800600-139802200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr6:139800600-139802200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:139800600-139804600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:139800600-139805200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:139800800-139801200	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:139800800-139801600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:139800800-139802200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:139800800-139802200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr6:139800800-139802400	Flanking Active TSS	HepG2	liver
26	chr6:139800800-139804400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:139800800-139805200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr6:139800800-139805200	Enhancers	Liver	Liver

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