Variant report

Variant	rs1920144
Chromosome Location	chr1:171110307-171110308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171109416..171111104-chr1:171115194..171116914,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10911192	0.88[CHD][hapmap]
rs10911839	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911841	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912425	0.89[ASN][1000 genomes]
rs1157459	0.85[GIH][hapmap]
rs11811455	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16864094	0.85[GIH][hapmap]
rs16864096	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920151	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920152	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920153	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920154	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064079	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064080	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2235193	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236872	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2236873	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2281003	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2281004	0.85[GIH][hapmap]
rs4916390	0.88[ASN][1000 genomes]
rs58365744	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67522662	0.89[ASN][1000 genomes]
rs7881379	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7885012	0.89[ASN][1000 genomes]
rs909530	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1920144	RP1-127D3.4	cis	Adipose Subcutaneous	GTEx
rs1920144	FMO2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171105400-171111200	Weak transcription	Aorta	Aorta
2	chr1:171105800-171110400	Enhancers	Fetal Lung	lung
3	chr1:171106400-171110400	Enhancers	Adipose Nuclei	Adipose
4	chr1:171107200-171110800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:171107200-171111200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:171107200-171111200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:171107200-171111400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:171107200-171111400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:171107800-171110400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:171107800-171112400	Enhancers	Fetal Muscle Leg	muscle
11	chr1:171108000-171112600	Weak transcription	Small Intestine	intestine
12	chr1:171108400-171112800	Enhancers	NHLF	lung
13	chr1:171108800-171111000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:171108800-171112400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:171108800-171112800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:171109000-171111200	Enhancers	Fetal Intestine Small	intestine
17	chr1:171109000-171112200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:171109000-171112200	Enhancers	Stomach Mucosa	stomach
19	chr1:171109200-171110400	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:171109200-171110600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:171109200-171111000	Enhancers	Fetal Intestine Large	intestine
22	chr1:171109200-171112000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:171109200-171112200	Weak transcription	Psoas Muscle	Psoas
24	chr1:171109200-171112400	Enhancers	Fetal Stomach	stomach
25	chr1:171109400-171110400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:171109400-171110400	Weak transcription	Brain Substantia Nigra	brain
27	chr1:171109400-171110400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:171109400-171110600	Weak transcription	Left Ventricle	heart
29	chr1:171109400-171111000	Enhancers	Liver	Liver
30	chr1:171109400-171111200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:171109400-171112000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:171109400-171112800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:171109600-171111200	Enhancers	Fetal Heart	heart
34	chr1:171109800-171110400	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:171109800-171110400	Enhancers	Stomach Smooth Muscle	stomach
36	chr1:171109800-171111800	Weak transcription	Brain Angular Gyrus	brain
37	chr1:171110000-171111000	Weak transcription	Ovary	ovary
38	chr1:171110200-171110400	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr1:171110200-171110600	Weak transcription	Right Atrium	heart
40	chr1:171110200-171110800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:171110200-171110800	Enhancers	Fetal Kidney	kidney
42	chr1:171110200-171111200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:171110200-171111200	Enhancers	Brain Cingulate Gyrus	brain
44	chr1:171110200-171111200	Enhancers	NHDF-Ad	bronchial
45	chr1:171110200-171111600	Enhancers	Brain Hippocampus Middle	brain
46	chr1:171110200-171112200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:171110200-171112400	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links