Variant report

Variant	rs12409137
Chromosome Location	chr1:10312124-10312125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1013952	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1013953	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10492969	0.96[ASN][1000 genomes]
rs10492971	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10492972	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10492973	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1065828	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10864448	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10864449	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864450	0.96[ASN][1000 genomes]
rs10864453	0.84[ASN][1000 genomes]
rs11121535	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11121537	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11121539	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11121541	0.80[ASN][1000 genomes]
rs11121545	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11121551	0.83[EUR][1000 genomes]
rs1138791	0.81[EUR][1000 genomes]
rs11576459	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11580789	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11580854	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11582123	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584023	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586842	0.82[EUR][1000 genomes]
rs12117635	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120042	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12120191	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12122029	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125535	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12127553	0.87[EUR][1000 genomes]
rs12127604	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130563	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12131441	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12132134	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12133617	0.96[ASN][1000 genomes]
rs12136404	0.96[ASN][1000 genomes]
rs12137456	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12137880	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12139981	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12141246	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12141416	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402052	0.82[EUR][1000 genomes]
rs12403465	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12406943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407992	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12408019	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12409933	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12722830	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12725210	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12737239	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12738317	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12753426	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12755094	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12757288	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1467653	0.80[ASN][1000 genomes]
rs1538557	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555849	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1556916	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1556917	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17034643	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17034821	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17396973	0.96[ASN][1000 genomes]
rs17402762	0.80[ASN][1000 genomes]
rs17410217	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1970379	0.92[ASN][1000 genomes]
rs2027327	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2027328	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2027329	0.83[ASN][1000 genomes]
rs2027330	0.90[ASN][1000 genomes]
rs2039778	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2105212	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2148152	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2182326	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2185252	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276100	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34565762	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34636442	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35257796	0.80[ASN][1000 genomes]
rs35388505	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35837142	0.81[EUR][1000 genomes]
rs35850116	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748575	0.94[ASN][1000 genomes]
rs3748577	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748579	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4240911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259656	0.81[EUR][1000 genomes]
rs4333852	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4475756	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4529713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845930	0.96[ASN][1000 genomes]
rs4845931	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845932	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4846197	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846198	0.96[ASN][1000 genomes]
rs4846199	0.96[ASN][1000 genomes]
rs4846205	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846207	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846208	0.82[EUR][1000 genomes]
rs4846209	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4846210	0.81[EUR][1000 genomes]
rs4846211	0.95[ASN][1000 genomes]
rs4846212	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4846213	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55676616	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58549151	0.82[EUR][1000 genomes]
rs61326491	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61775872	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61775874	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61775885	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61775887	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61778376	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61778399	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61778401	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61778402	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61778403	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6541084	0.96[ASN][1000 genomes]
rs6541085	0.96[ASN][1000 genomes]
rs6541089	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6541090	0.84[ASN][1000 genomes]
rs6685895	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700866	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7368073	0.90[ASN][1000 genomes]
rs746881	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524693	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524908	0.96[ASN][1000 genomes]
rs7546364	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7546368	0.80[ASN][1000 genomes]
rs7547513	0.94[ASN][1000 genomes]
rs7553228	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553935	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8019	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs912961	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs912962	0.94[ASN][1000 genomes]
rs912963	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332414	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs946501	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946502	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946503	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946504	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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv999251	chr1:10276263-10318163	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv545382	chr1:10309026-10377221	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12409137	KIF1B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10272600-10368200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10277000-10322000	Weak transcription	Spleen	Spleen
3	chr1:10285200-10316000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:10285400-10312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:10287400-10312400	Weak transcription	Pancreas	Pancrea
6	chr1:10289200-10317400	Weak transcription	Liver	Liver
7	chr1:10293000-10322000	Weak transcription	Primary T cells from cord blood	blood
8	chr1:10295600-10316400	Weak transcription	Placenta	Placenta
9	chr1:10295600-10317600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:10295800-10322000	Weak transcription	Lung	lung
11	chr1:10296200-10312400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:10296200-10313600	Weak transcription	Fetal Brain Female	brain
13	chr1:10296400-10312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:10296400-10313200	Weak transcription	Fetal Stomach	stomach
15	chr1:10296400-10316800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:10297200-10316200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:10297200-10316200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:10297400-10312400	Weak transcription	NHLF	lung
19	chr1:10297400-10316200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:10297600-10312400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:10297800-10312400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:10298000-10312400	Weak transcription	HepG2	liver
23	chr1:10298400-10312400	Weak transcription	Right Atrium	heart
24	chr1:10302000-10313200	Weak transcription	Fetal Heart	heart
25	chr1:10302000-10321800	Weak transcription	Esophagus	oesophagus
26	chr1:10302200-10313800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:10302400-10312600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:10302400-10315600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:10302600-10313200	Weak transcription	Fetal Kidney	kidney
30	chr1:10303200-10313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:10303200-10316000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr1:10305200-10313200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:10305200-10317200	Weak transcription	Brain Germinal Matrix	brain
34	chr1:10306200-10312600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:10306200-10313400	Weak transcription	Fetal Intestine Large	intestine
36	chr1:10306200-10313600	Weak transcription	Ovary	ovary
37	chr1:10306200-10316000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:10307400-10313200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:10307600-10312400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:10307600-10340400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:10307800-10316200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:10308400-10316200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:10308600-10314200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:10308800-10314400	Enhancers	Brain Substantia Nigra	brain
45	chr1:10309000-10312400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:10309600-10315400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:10309800-10312400	Weak transcription	Adipose Nuclei	Adipose
48	chr1:10309800-10313800	Enhancers	Psoas Muscle	Psoas
49	chr1:10310000-10312400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:10310000-10313400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links