Variant report

Variant	rs12971000
Chromosome Location	chr18:12457679-12457680
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12451035..12453688-chr18:12457472..12459891,2	K562	blood:
2	chr18:12457149..12459237-chr18:12472773..12475117,2	K562	blood:

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11664013	1.00[CHD][hapmap]
rs12954350	1.00[ASN][1000 genomes]
rs12954606	1.00[ASN][1000 genomes]
rs12955162	1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957283	1.00[ASN][1000 genomes]
rs12958301	1.00[ASN][1000 genomes]
rs12959459	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961307	1.00[CHD][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	1.00[ASN][1000 genomes]
rs17524639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525318	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17525459	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17525599	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17615525	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615801	1.00[CHD][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs17615991	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17616124	1.00[ASN][1000 genomes]
rs34054541	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34088731	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34180475	1.00[ASN][1000 genomes]
rs34215298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34229934	1.00[ASN][1000 genomes]
rs34371240	1.00[ASN][1000 genomes]
rs34448712	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34460164	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34469203	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503700	1.00[ASN][1000 genomes]
rs34512782	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34620743	0.87[EUR][1000 genomes]
rs34737110	1.00[ASN][1000 genomes]
rs34933611	1.00[ASN][1000 genomes]
rs35160505	1.00[ASN][1000 genomes]
rs35190325	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35532404	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	1.00[ASN][1000 genomes]
rs35744165	1.00[ASN][1000 genomes]
rs35826479	1.00[ASN][1000 genomes]
rs35872229	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs71351482	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351484	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351485	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351491	1.00[ASN][1000 genomes]
rs71351492	1.00[ASN][1000 genomes]
rs71351494	1.00[ASN][1000 genomes]
rs71351495	1.00[ASN][1000 genomes]
rs71351501	1.00[ASN][1000 genomes]
rs71363149	1.00[ASN][1000 genomes]
rs919	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12971000	SLMO1	cis	Thyroid	GTEx
rs12971000	SLMO1	cis	Nerve Tibial	GTEx
rs12971000	SLMO1	cis	Adipose Subcutaneous	GTEx
rs12971000	RP11-861E21.2	cis	Thyroid	GTEx
rs12971000	SLMO1	cis	cerebellum	SCAN
rs12971000	SLMO1	cis	Esophagus Muscularis	GTEx
rs12971000	SLMO1	cis	lung	GTEx
rs12971000	AP001029.1	cis	Thyroid	GTEx
rs12971000	AP001029.1	cis	Artery Tibial	GTEx
rs12971000	AP001029.1	cis	Artery Aorta	GTEx
rs12971000	SLMO1	cis	Esophagus Mucosa	GTEx
rs12971000	RP11-861E21.1	cis	Esophagus Muscularis	GTEx
rs12971000	AP001029.1	cis	Esophagus Muscularis	GTEx
rs12971000	SLMO1	cis	Artery Aorta	GTEx
rs12971000	SLMO1	cis	Artery Tibial	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:12433400-12458600	Weak transcription	HepG2	liver
4	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
5	chr18:12439400-12468200	Weak transcription	K562	blood
6	chr18:12442000-12459200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:12444000-12460200	Weak transcription	Fetal Intestine Large	intestine
8	chr18:12444000-12467400	Weak transcription	A549	lung
9	chr18:12444200-12463200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:12444400-12458600	Weak transcription	Fetal Heart	heart
11	chr18:12444400-12465800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr18:12444600-12459400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr18:12444600-12477600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr18:12445600-12459200	Weak transcription	Fetal Intestine Small	intestine
15	chr18:12445600-12460800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr18:12445800-12459000	Weak transcription	Placenta	Placenta
17	chr18:12446200-12479600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr18:12447000-12460800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr18:12447800-12459200	Weak transcription	Fetal Lung	lung
20	chr18:12447800-12461200	Weak transcription	Colon Smooth Muscle	Colon
21	chr18:12448000-12463000	Weak transcription	Psoas Muscle	Psoas
22	chr18:12449600-12458600	Weak transcription	NHDF-Ad	bronchial
23	chr18:12449600-12459200	Weak transcription	NHLF	lung
24	chr18:12449600-12470600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr18:12449600-12477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:12449800-12459200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr18:12449800-12459400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr18:12449800-12461000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr18:12449800-12461000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr18:12449800-12465400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr18:12449800-12466800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr18:12449800-12470600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr18:12449800-12477600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr18:12449800-12477600	Weak transcription	Spleen	Spleen
35	chr18:12449800-12477800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr18:12449800-12478000	Weak transcription	Gastric	stomach
37	chr18:12449800-12478000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr18:12449800-12479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr18:12450000-12460800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr18:12450000-12478200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr18:12451000-12457800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr18:12452200-12464600	Weak transcription	Pancreas	Pancrea
43	chr18:12452400-12459200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr18:12452600-12458600	Weak transcription	HUVEC	blood vessel
45	chr18:12452600-12458800	Weak transcription	Right Ventricle	heart
46	chr18:12452600-12458800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr18:12452600-12459200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr18:12452600-12459200	Weak transcription	Aorta	Aorta
49	chr18:12452800-12458800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr18:12452800-12459400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links