Variant report

Variant	rs10890406
Chromosome Location	chr1:47068677-47068678
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47054632..47056967-chr1:47067428..47069828,2	K562	blood:
2	chr1:47053775..47056193-chr1:47067460..47069823,2	MCF-7	breast:
3	chr1:47066512..47069474-chr1:47070954..47073416,4	K562	blood:
4	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:
5	chr1:47068203..47069866-chr1:47187301..47190738,3	MCF-7	breast:
6	chr1:47053959..47056132-chr1:47066697..47069062,3	K562	blood:
7	chr1:47033343..47035201-chr1:47067108..47069992,2	K562	blood:
8	chr1:47041717..47044206-chr1:47067000..47069818,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction
ENSG00000142961	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10890407	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10890408	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211319	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11211320	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211323	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11211324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211325	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211326	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11211327	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12022855	1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12136479	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1258010	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258012	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258022	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258050	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258051	1.00[CHB][hapmap]
rs1767612	1.00[CHB][hapmap]
rs2297850	0.93[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs35494693	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36058295	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275405	1.00[CEU][hapmap]
rs4660357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660947	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671527	0.88[ASW][hapmap];0.93[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6687832	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704020	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7526249	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7526328	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs942083	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs946321	1.00[CHB][hapmap]
rs956526	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs956527	1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3409996	chr1:47068523-47068987	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10890406	MMACHC	cis	cerebellum	SCAN
rs10890406	C1orf84	cis	cerebellum	SCAN
rs10890406	FAM183A	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47042600-47069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:47042800-47068800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:47045600-47068800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:47046200-47069000	Weak transcription	Fetal Kidney	kidney
5	chr1:47048400-47069000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:47055400-47068800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:47056600-47068800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:47057000-47069000	Weak transcription	NH-A	brain
9	chr1:47057600-47069000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:47058600-47069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:47059000-47068800	Weak transcription	Ovary	ovary
12	chr1:47059000-47068800	Weak transcription	HUVEC	blood vessel
13	chr1:47059200-47068800	Weak transcription	A549	lung
14	chr1:47059800-47068800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:47059800-47068800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:47059800-47069000	Weak transcription	HSMMtube	muscle
17	chr1:47060000-47068800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:47060000-47068800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:47060000-47068800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:47060000-47069000	Weak transcription	Fetal Intestine Small	intestine
21	chr1:47060000-47069000	Weak transcription	Fetal Stomach	stomach
22	chr1:47060400-47069000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:47061200-47068800	Weak transcription	HSMM	muscle
24	chr1:47065200-47068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:47065400-47068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:47065800-47068800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:47065800-47069000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:47065800-47069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:47065800-47069200	Weak transcription	Small Intestine	intestine
30	chr1:47066400-47068800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:47066400-47068800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:47066400-47068800	Weak transcription	NHLF	lung
33	chr1:47067000-47068800	Enhancers	HepG2	liver
34	chr1:47067000-47069000	Enhancers	Left Ventricle	heart
35	chr1:47067000-47069200	Enhancers	Lung	lung
36	chr1:47067000-47069400	Enhancers	Stomach Mucosa	stomach
37	chr1:47067200-47068800	Enhancers	Colon Smooth Muscle	Colon
38	chr1:47067200-47069000	Enhancers	Gastric	stomach
39	chr1:47067400-47068800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:47067400-47068800	Enhancers	Right Ventricle	heart
41	chr1:47067400-47068800	Enhancers	Dnd41	blood
42	chr1:47067600-47069600	Enhancers	Spleen	Spleen
43	chr1:47067800-47068800	Weak transcription	Fetal Intestine Large	intestine
44	chr1:47068000-47069000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:47068200-47068800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:47068200-47069000	Enhancers	K562	blood
47	chr1:47068200-47069400	Flanking Active TSS	Pancreas	Pancrea
48	chr1:47068400-47068800	Enhancers	Brain Angular Gyrus	brain
49	chr1:47068400-47068800	Active TSS	Brain Substantia Nigra	brain
50	chr1:47068400-47068800	Enhancers	HMEC	breast

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