Variant report

Variant	rs3095294
Chromosome Location	chr6:29628037-29628038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs2535238	0.88[ASN][1000 genomes]
rs2747421	0.88[ASN][1000 genomes]
rs2747427	0.88[ASN][1000 genomes]
rs2747428	0.88[ASN][1000 genomes]
rs2747429	0.88[ASN][1000 genomes]
rs29218	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29228	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3094579	0.87[ASN][1000 genomes]
rs3095266	0.84[ASN][1000 genomes]
rs3095269	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3095271	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095290	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3117289	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3117318	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129058	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129062	0.88[ASN][1000 genomes]
rs3129063	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129069	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129073	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130251	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs374317	0.88[ASN][1000 genomes]
rs375248	0.87[ASN][1000 genomes]
rs375984	0.88[ASN][1000 genomes]
rs376319	0.88[ASN][1000 genomes]
rs387640	0.88[ASN][1000 genomes]
rs387642	0.88[ASN][1000 genomes]
rs417764	0.88[ASN][1000 genomes]
rs448380	0.87[ASN][1000 genomes]
rs448489	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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3095294	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3095294	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs3095294	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3095294	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29618400-29629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:29618400-29629600	Weak transcription	Right Ventricle	heart
3	chr6:29620000-29628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:29620000-29631200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:29623400-29630600	Active TSS	Brain Anterior Caudate	brain
6	chr6:29624400-29629200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:29624400-29630400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:29624600-29628600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:29624600-29628600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:29624800-29628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:29624800-29628800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:29624800-29629000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:29624800-29631600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:29625000-29628800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:29625000-29628800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:29625000-29628800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:29625000-29629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:29625000-29629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
20	chr6:29625200-29628800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:29625200-29628800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:29626600-29631400	Weak transcription	Fetal Heart	heart
23	chr6:29627200-29628400	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
24	chr6:29627800-29629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:29628000-29628800	Weak transcription	Brain Angular Gyrus	brain
26	chr6:29628000-29628800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:29628000-29628800	Weak transcription	Brain Substantia Nigra	brain
28	chr6:29628000-29630200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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