Variant report

Variant	rs12141407
Chromosome Location	chr1:212659654-212659655
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212646367..212648750-chr1:212657386..212659832,2	K562	blood:
2	chr1:212654477..212657612-chr1:212658521..212662499,5	K562	blood:
3	chr1:212657352..212659830-chr1:212670221..212673074,2	K562	blood:
4	chr1:212658367..212661601-chr1:212781233..212783647,4	MCF-7	breast:
5	chr1:212659642..212660199-chr1:212731505..212732148,2	Hela-S3	cervix:
6	chr1:212657965..212660283-chr1:212780837..212783197,2	MCF-7	breast:
7	chr1:212657982..212660814-chr1:212768286..212770089,2	K562	blood:
8	chr1:212648507..212667078-chr1:212779147..212787651,52	K562	blood:
9	chr1:212652289..212653872-chr1:212658480..212660402,2	K562	blood:
10	chr1:212657477..212661646-chr1:212730263..212734721,4	K562	blood:
11	chr1:212645024..212669819-chr1:212778382..212791615,68	K562	blood:
12	chr1:212651212..212653872-chr1:212658074..212660402,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260805	Chromatin interaction
ENSG00000264590	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12131037	0.88[EUR][1000 genomes]
rs12135668	0.96[EUR][1000 genomes]
rs12729438	1.00[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs12741983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13374785	0.86[EUR][1000 genomes]
rs3001262	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34543166	0.88[EUR][1000 genomes]
rs36056520	0.86[EUR][1000 genomes]
rs525176	0.86[EUR][1000 genomes]
rs557252	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs572235	0.96[ASN][1000 genomes]
rs590156	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs591176	0.95[EUR][1000 genomes]
rs624387	0.86[EUR][1000 genomes]
rs626178	0.89[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs638527	0.87[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs653006	0.86[EUR][1000 genomes]
rs653532	0.86[EUR][1000 genomes]
rs6540742	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6540743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6669813	0.98[EUR][1000 genomes]
rs6694514	0.97[ASN][1000 genomes]
rs679840	0.87[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs748517	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7513550	0.88[EUR][1000 genomes]
rs7515863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7529867	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7537826	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7553229	0.89[EUR][1000 genomes]
rs796930	0.85[EUR][1000 genomes]
rs806539	0.83[EUR][1000 genomes]
rs9430096	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
5	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv873163	chr1:212629935-212669475	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
12	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12141407	C1orf74	cis	parietal	SCAN
rs12141407	PIGR	cis	parietal	SCAN
rs12141407	TMEM206	cis	cerebellum	SCAN
rs12141407	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212650600-212667800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:212650800-212661600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:212655000-212665800	Enhancers	Placenta	Placenta
4	chr1:212655200-212660200	Enhancers	Fetal Intestine Large	intestine
5	chr1:212655200-212662800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:212655400-212660000	Enhancers	HSMM	muscle
7	chr1:212655400-212660200	Enhancers	NH-A	brain
8	chr1:212655600-212662200	Weak transcription	Right Atrium	heart
9	chr1:212656400-212661600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:212656400-212661600	Weak transcription	Aorta	Aorta
11	chr1:212656400-212662000	Weak transcription	Left Ventricle	heart
12	chr1:212656800-212661400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:212656800-212661800	Weak transcription	Colonic Mucosa	Colon
14	chr1:212656800-212662200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:212657200-212664800	Weak transcription	Spleen	Spleen
16	chr1:212657400-212660200	Enhancers	Fetal Intestine Small	intestine
17	chr1:212657400-212660200	Enhancers	HMEC	breast
18	chr1:212657400-212660200	Enhancers	Osteobl	bone
19	chr1:212657600-212660000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:212657600-212660000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:212657800-212659800	Enhancers	HUVEC	blood vessel
22	chr1:212657800-212660000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:212658000-212660000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:212658000-212660000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:212658000-212660000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:212658000-212660000	Enhancers	HSMMtube	muscle
27	chr1:212658000-212660000	Enhancers	NHDF-Ad	bronchial
28	chr1:212658000-212662800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:212658000-212663000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:212658000-212663000	Enhancers	Stomach Mucosa	stomach
31	chr1:212658200-212660000	Flanking Active TSS	A549	lung
32	chr1:212658200-212660000	Enhancers	NHEK	skin
33	chr1:212658200-212660200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:212658200-212660200	Flanking Active TSS	Hela-S3	cervix
35	chr1:212658200-212663000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:212658400-212660000	Enhancers	K562	blood
37	chr1:212658400-212660200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:212658600-212660000	Enhancers	Esophagus	oesophagus
39	chr1:212658600-212660200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:212658600-212660200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr1:212658800-212660200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr1:212658800-212660200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr1:212658800-212660200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:212658800-212660600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:212659000-212659800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:212659000-212659800	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:212659000-212660000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:212659000-212660000	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr1:212659000-212660000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:212659000-212660200	Enhancers	Rectal Mucosa Donor 31	rectum

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