Variant report

Variant	rs9943281
Chromosome Location	chr1:151878223-151878224
allele	G/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	chr1:151861522..151872673-chr1:151876647..151885029,20	MCF-7	breast:
2	chr1:151875998..151878434-chr1:151880509..151883027,2	MCF-7	breast:
3	chr1:151869363..151871176-chr1:151876802..151879330,2	K562	blood:
4	chr1:151869400..151872007-chr1:151876004..151878841,3	K562	blood:
5	chr1:151877897..151883557-chr1:152019456..152022411,7	K562	blood:
6	chr1:151843538..151846125-chr1:151876423..151878232,2	K562	blood:
7	chr1:151875575..151878356-chr1:151906918..151909478,2	MCF-7	breast:
8	chr1:151877100..151879105-chr1:151904662..151907156,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1038747	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1060870	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10788817	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10788818	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10788820	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888445	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11204914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204915	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11589720	0.86[ASN][1000 genomes]
rs12067594	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12116923	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12562586	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13320	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1387833	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1490189	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1907040	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2130525	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279501	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279502	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2338201	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2338209	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932565	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932576	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932577	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932579	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2932581	0.84[ASN][1000 genomes]
rs2932583	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2932586	0.87[ASN][1000 genomes]
rs2999506	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999508	0.84[ASN][1000 genomes]
rs2999512	0.84[ASN][1000 genomes]
rs2999541	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999542	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999544	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999545	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999546	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007670	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007685	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007691	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3007711	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845409	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845713	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685187	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6698740	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7523082	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7541453	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7542137	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9435963	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9435964	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription 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 target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9943281	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs9943281	THEM4	cis	Nerve Tibial	GTEx
rs9943281	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs9943281	THEM4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151841200-151880800	Weak transcription	NHLF	lung
3	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
4	chr1:151854000-151880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:151860800-151879800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:151861600-151879800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:151862400-151880400	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:151864800-151881400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:151866200-151879600	Weak transcription	NHDF-Ad	bronchial
10	chr1:151866200-151880200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:151866600-151879800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:151867200-151879600	Weak transcription	Fetal Stomach	stomach
13	chr1:151867400-151878600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:151868000-151879800	Weak transcription	Liver	Liver
15	chr1:151868000-151880200	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:151868000-151880400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:151868000-151880800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:151871400-151878800	Weak transcription	Lung	lung
19	chr1:151871400-151878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:151871400-151879800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:151871400-151880400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:151871800-151878800	Weak transcription	Thymus	Thymus
23	chr1:151872800-151880800	Weak transcription	Right Atrium	heart
24	chr1:151873000-151880800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:151874400-151878600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:151874800-151880400	Weak transcription	Brain Anterior Caudate	brain
27	chr1:151875000-151879600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:151875000-151879800	Weak transcription	Fetal Lung	lung
29	chr1:151875400-151878400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:151875400-151878400	Weak transcription	Pancreas	Pancrea
31	chr1:151875400-151879600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:151875400-151879600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:151875800-151879600	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:151876400-151879600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:151876600-151881400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:151876800-151879200	Enhancers	Fetal Intestine Large	intestine
37	chr1:151877000-151878400	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr1:151877000-151878600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr1:151877000-151880800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:151877200-151878400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr1:151877200-151878400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:151877200-151878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:151877200-151878400	Enhancers	Adipose Nuclei	Adipose
44	chr1:151877200-151878400	Strong transcription	A549	lung
45	chr1:151877200-151878600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:151877200-151879000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr1:151877400-151879200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:151877400-151879200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:151877400-151879200	Genic enhancers	Fetal Intestine Small	intestine
50	chr1:151877600-151878400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links