Variant report

Variant	rs1012629
Chromosome Location	chr6:128769900-128769901
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THEMIS-2	chr6:128768789-128770446	ENSG00000182404.5
2	lnc-THEMIS-2	chr6:128768543-128770446	ENSG00000182404.6

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10872331	1.00[CHD][hapmap]
rs11154439	1.00[CHD][hapmap]
rs11756545	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17364020	1.00[CHD][hapmap]
rs17364090	1.00[CHD][hapmap]
rs17364118	1.00[CHD][hapmap]
rs17459694	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17460765	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17460940	0.94[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461178	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461290	0.88[CEU][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs17461370	1.00[CHD][hapmap]
rs1935130	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326702	1.00[CHD][hapmap]
rs55848328	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62425728	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425730	1.00[ASN][1000 genomes]
rs62425732	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62425734	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425736	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482886	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491959	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491965	0.89[TSI][hapmap]
rs9492002	1.00[CHD][hapmap]
rs9492021	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1012629	AKAP7	cis	parietal	SCAN
rs1012629	MOXD1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128740800-128777000	Weak transcription	Fetal Intestine Small	intestine
2	chr6:128753200-128777000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:128756400-128776600	Weak transcription	Fetal Intestine Large	intestine
4	chr6:128759800-128786800	Weak transcription	Left Ventricle	heart
5	chr6:128761400-128775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:128761400-128778000	Weak transcription	Small Intestine	intestine
7	chr6:128762800-128774800	Weak transcription	Ovary	ovary
8	chr6:128763000-128771800	Weak transcription	Fetal Kidney	kidney
9	chr6:128763200-128773200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:128763600-128775200	Weak transcription	Psoas Muscle	Psoas
11	chr6:128765600-128775200	Weak transcription	Pancreas	Pancrea
12	chr6:128765800-128777000	Weak transcription	HepG2	liver
13	chr6:128767400-128773600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:128767800-128785200	Weak transcription	NHEK	skin
15	chr6:128768000-128771000	Weak transcription	Fetal Brain Male	brain
16	chr6:128768000-128773200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:128768200-128785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:128768400-128770400	Weak transcription	Fetal Brain Female	brain
19	chr6:128769000-128770400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:128769200-128770000	Enhancers	Fetal Heart	heart
21	chr6:128769400-128771600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:128769600-128770000	Enhancers	Brain Hippocampus Middle	brain

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