Variant report

Variant	rs12046208
Chromosome Location	chr1:113171589-113171590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113171507-113171677	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113170754..113173551-chr1:113190462..113192444,2	MCF-7	breast:
2	chr1:113167056..113168911-chr1:113169739..113172643,2	MCF-7	breast:
3	chr1:113160723..113165186-chr1:113170921..113177730,6	MCF-7	breast:
4	chr1:113167976..113172227-chr1:113246480..113250465,5	K562	blood:

Variant related genes	Relation type
MRPL53P1	TF binding region
ENSG00000235299	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155366	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10745330	0.89[CEU][hapmap];0.83[GIH][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap]
rs10776755	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs10776757	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857963	0.89[CEU][hapmap]
rs1110043	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11584092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042407	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12126277	0.89[CEU][hapmap]
rs12728001	0.85[CEU][hapmap]
rs2932532	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2932536	0.88[CEU][hapmap];0.83[GIH][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap]
rs2999154	0.85[CEU][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs2999155	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs2999156	0.91[GIH][hapmap]
rs3013439	0.87[CEU][hapmap]
rs3013440	0.89[CEU][hapmap]
rs351372	0.85[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap]
rs4838959	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4839254	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55675817	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537748	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537749	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs663533	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6666579	0.89[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs6682737	0.89[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs6700673	0.88[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap]
rs72699100	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7415820	0.89[CEU][hapmap];0.83[GIH][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs7512948	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7513716	0.88[CEU][hapmap]
rs7522288	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544663	0.89[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs7554916	0.85[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]
rs902289	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs910697	0.85[CEU][hapmap]
rs937053	0.85[ASN][1000 genomes]
rs9429486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
6	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer 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	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs12046208	ST7L	cis	lymphoblastoid	seeQTL
rs12046208	ST7L	cis	Lymphoblastoid	GTEx
rs12046208	ST7L	cis	Thyroid	GTEx
rs12046208	C1orf162	cis	parietal	SCAN
rs12046208	KCNA10	cis	parietal	SCAN
rs12046208	ST7L	cis	Nerve Tibial	GTEx
rs12046208	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs12046208	CTTNBP2NL	cis	parietal	SCAN
rs12046208	ST7L	cis	multi-tissue	Pritchard
rs12046208	ST7L	cis	Esophagus Muscularis	GTEx
rs12046208	ST7L	cis	Artery Tibial	GTEx
rs12046208	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs12046208	ST7L	cis	lung	GTEx
rs12046208	ST7L	cis	normal skin	skin_eQTL
rs12046208	SYCP1	cis	parietal	SCAN
rs12046208	ALX3	cis	parietal	SCAN
rs12046208	ST7L	cis	lesional skin	skin_eQTL
rs12046208	WNT2B	cis	parietal	SCAN
rs12046208	ST7L	cis	uninvolved skin	skin_eQTL
rs12046208	ST7L	cis	Adipose Subcutaneous	GTEx
rs12046208	ST7L	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113163600-113171600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:113163600-113173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:113163600-113180600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:113163600-113200000	Weak transcription	Fetal Kidney	kidney
5	chr1:113163800-113173200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:113163800-113176000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:113163800-113200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:113163800-113200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:113164000-113173200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:113164000-113190000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:113164200-113175800	Weak transcription	Fetal Brain Female	brain
12	chr1:113164200-113180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
14	chr1:113164800-113179200	Weak transcription	Colonic Mucosa	Colon
15	chr1:113165200-113172200	Weak transcription	Brain Germinal Matrix	brain
16	chr1:113165400-113174400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:113165400-113175200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:113165400-113176400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:113165600-113174400	Genic enhancers	K562	blood
20	chr1:113166000-113173200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:113167400-113173600	Genic enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:113167800-113176200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr1:113168000-113180000	Weak transcription	Aorta	Aorta
24	chr1:113168600-113171600	Enhancers	Adipose Nuclei	Adipose
25	chr1:113168600-113171800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:113168600-113171800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:113168600-113172800	Strong transcription	Hela-S3	cervix
28	chr1:113168600-113173200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:113168600-113173400	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:113168600-113177800	Weak transcription	Fetal Intestine Large	intestine
31	chr1:113168600-113179200	Weak transcription	NH-A	brain
32	chr1:113168800-113171800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:113168800-113172000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:113168800-113172000	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:113168800-113172800	Weak transcription	Thymus	Thymus
36	chr1:113168800-113173000	Weak transcription	Pancreas	Pancrea
37	chr1:113168800-113173400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:113168800-113174000	Weak transcription	Psoas Muscle	Psoas
39	chr1:113168800-113174800	Weak transcription	Right Atrium	heart
40	chr1:113168800-113177600	Weak transcription	Stomach Mucosa	stomach
41	chr1:113168800-113177800	Weak transcription	NHLF	lung
42	chr1:113168800-113178200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:113168800-113179200	Weak transcription	Brain Angular Gyrus	brain
44	chr1:113168800-113179200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:113168800-113179200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:113168800-113179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:113168800-113180000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:113168800-113180000	Weak transcription	Lung	lung
49	chr1:113168800-113187200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:113168800-113189800	Weak transcription	Fetal Lung	lung

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