Variant report

Variant	rs12116923
Chromosome Location	chr1:151919326-151919327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151911549..151914753-chr1:151917047..151920046,3	K562	blood:
2	chr1:151918412..151920135-chr1:151920921..151922803,2	K562	blood:
3	chr1:151914726..151916924-chr1:151917247..151919609,3	MCF-7	breast:
4	chr1:151915835..151920651-chr1:152004121..152010886,7	MCF-7	breast:
5	chr1:151917183..151919501-chr1:152008114..152010423,2	K562	blood:
6	chr1:151918309..151920987-chr1:151938809..151942058,3	MCF-7	breast:
7	chr1:151912762..151919992-chr1:151963219..151969467,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1038747	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10494270	0.85[CHB][hapmap]
rs1060870	0.85[AMR][1000 genomes]
rs10788817	0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10788818	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10788820	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11204914	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204915	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204922	0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11589720	0.98[ASN][1000 genomes]
rs12067594	0.86[AMR][1000 genomes]
rs12083193	0.81[CHB][hapmap]
rs12562586	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1387833	0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1490189	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16833668	0.90[CHB][hapmap]
rs16833728	0.86[CHB][hapmap]
rs1907040	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2130525	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279501	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279502	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2337689	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2338019	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2338201	0.85[AMR][1000 genomes]
rs2338209	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2932565	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2932570	0.86[JPT][hapmap]
rs2932576	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2932577	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2932579	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932581	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932583	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932586	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932590	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2999506	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2999508	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999512	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999526	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2999528	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2999531	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2999534	0.85[JPT][hapmap]
rs2999539	0.85[JPT][hapmap]
rs2999541	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2999542	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2999544	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2999545	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2999546	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3007670	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3007685	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3007691	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3007708	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3007711	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4845409	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4845713	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6587635	0.82[CHB][hapmap]
rs6587636	0.82[CHB][hapmap]
rs6587637	0.80[JPT][hapmap]
rs6587638	0.80[CHB][hapmap]
rs6587640	0.81[CHB][hapmap]
rs6662611	0.82[CHB][hapmap]
rs6663064	0.90[CHB][hapmap]
rs6678672	0.81[CHB][hapmap]
rs6685187	0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs6686874	0.90[CHB][hapmap]
rs6698740	0.85[AMR][1000 genomes]
rs6703465	0.82[CHB][hapmap]
rs7535002	0.86[CHB][hapmap]
rs7541099	0.86[CHB][hapmap]
rs7542137	0.86[AMR][1000 genomes]
rs902313	0.86[CHB][hapmap]
rs9435963	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9435964	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs971887	0.82[CHB][hapmap]
rs9943221	0.86[CHB][hapmap]
rs9943251	0.88[CHB][hapmap]
rs9943281	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12116923	THEM4	cis	multi-tissue	Pritchard
rs12116923	THEM4	cis	Nerve Tibial	GTEx
rs12116923	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs12116923	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs12116923	THEM4	cis	Esophagus Muscularis	GTEx
rs12116923	S100A10	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151913000-151919800	Enhancers	Fetal Intestine Large	intestine
2	chr1:151914000-151922000	Weak transcription	Spleen	Spleen
3	chr1:151915200-151919600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:151915600-151919400	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:151916200-151919600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:151916400-151919400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:151916400-151919600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:151916400-151919800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:151916600-151919400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:151916600-151919400	Enhancers	Colon Smooth Muscle	Colon
11	chr1:151916600-151919600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:151916600-151919600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:151916600-151919600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:151916600-151919600	Enhancers	Fetal Muscle Leg	muscle
15	chr1:151916600-151919600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:151916600-151919600	Enhancers	Stomach Mucosa	stomach
17	chr1:151916600-151919800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:151916600-151919800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr1:151916600-151919800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:151916600-151919800	Enhancers	Fetal Intestine Small	intestine
21	chr1:151916800-151919400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:151916800-151919600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr1:151916800-151919600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr1:151916800-151919800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:151916800-151919800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:151916800-151919800	Enhancers	HSMM	muscle
27	chr1:151916800-151919800	Enhancers	NHLF	lung
28	chr1:151916800-151920600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:151917000-151919400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr1:151917000-151919600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr1:151917000-151919600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:151917000-151919600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr1:151917000-151920200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:151917200-151919600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:151917200-151919800	Enhancers	HSMMtube	muscle
36	chr1:151917400-151919600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:151917400-151919600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:151917400-151919600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr1:151917600-151919800	Enhancers	NH-A	brain
40	chr1:151917600-151921800	Weak transcription	Lung	lung
41	chr1:151917600-151921800	Weak transcription	Pancreas	Pancrea
42	chr1:151917800-151919400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr1:151917800-151919400	Weak transcription	Esophagus	oesophagus
44	chr1:151917800-151919600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:151918000-151919400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr1:151918000-151920000	Enhancers	Osteobl	bone
47	chr1:151918200-151919600	Flanking Active TSS	NHEK	skin
48	chr1:151918200-151919800	Enhancers	Rectal Smooth Muscle	rectum
49	chr1:151918200-151920400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:151918600-151919600	Weak transcription	Gastric	stomach

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