Variant report

Variant	rs3010296
Chromosome Location	chr6:139797695-139797696
allele	A/G
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:139693565..139697388-chr6:139794842..139800531,8	K562	blood:
2	chr6:139797675..139799727-chr6:139800146..139801985,2	K562	blood:
3	chr6:139693348..139695724-chr6:139794532..139798166,3	K562	blood:
4	chr6:139795946..139798274-chr6:139802764..139804469,2	MCF-7	breast:
5	chr6:139795343..139797706-chr6:139807680..139810551,2	K562	blood:
6	chr6:139788753..139790765-chr6:139796325..139798435,2	K562	blood:
7	chr6:139793418..139795524-chr6:139796922..139799226,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238099	Chromatin interaction
ENSG00000164442	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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2908496	0.81[JPT][hapmap]
rs2908508	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]
rs3010289	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3010291	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3010292	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3010293	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010294	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3010295	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][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];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139794000-139799800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr6:139795800-139798000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:139795800-139799800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:139795800-139799800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:139795800-139799800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr6:139796000-139799400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr6:139796200-139797800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:139796200-139797800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:139796200-139799400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:139796200-139800600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:139796600-139800600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:139796600-139800800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:139796800-139797800	Weak transcription	HepG2	liver
14	chr6:139796800-139798400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:139796800-139799000	Enhancers	K562	blood
16	chr6:139796800-139800600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:139796800-139800800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:139796800-139800800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:139796800-139800800	Weak transcription	Liver	Liver
20	chr6:139796800-139801000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:139796800-139806600	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:139797000-139798000	Weak transcription	Fetal Intestine Large	intestine
23	chr6:139797000-139798800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:139797000-139806800	Weak transcription	Fetal Lung	lung
25	chr6:139797200-139798400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:139797200-139800400	Weak transcription	Fetal Stomach	stomach
27	chr6:139797200-139803200	Weak transcription	Fetal Kidney	kidney
28	chr6:139797400-139797800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:139797600-139798600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:139797600-139798600	Enhancers	Fetal Intestine Small	intestine
31	chr6:139797600-139799200	Enhancers	Brain Germinal Matrix	brain
32	chr6:139797600-139803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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