Variant report

Variant	rs232787
Chromosome Location	chr1:59130407-59130408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59125952..59132730-chr1:59132819..59139059,8	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11207290	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207291	0.92[EUR][1000 genomes]
rs11576713	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12123717	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12139211	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12144224	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12409869	0.82[CEU][hapmap]
rs12732648	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746851	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492718	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565662	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17117956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118103	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17118106	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1961788	0.95[ASN][1000 genomes]
rs232777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232782	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232854	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232855	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232865	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232866	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232870	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232881	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232884	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232887	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232888	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232889	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232890	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232891	0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232895	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232896	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232897	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232898	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232899	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232900	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232903	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232912	0.81[ASN][1000 genomes]
rs23588	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34941709	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35091401	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4912202	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4912362	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912368	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs516957	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6587835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587837	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664947	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700413	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs232787	MYSM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59115000-59132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:59115600-59138400	Weak transcription	Small Intestine	intestine
3	chr1:59116000-59151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:59116400-59137800	Weak transcription	Fetal Heart	heart
5	chr1:59116800-59131400	Weak transcription	Fetal Stomach	stomach
6	chr1:59117800-59147600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:59118000-59139000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:59118200-59163400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:59118600-59147400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:59119000-59135200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:59119800-59147600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:59119800-59155000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:59119800-59162200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:59119800-59163200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:59120000-59143000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:59120000-59153400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:59120200-59149400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:59121000-59161200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:59121200-59141600	Strong transcription	Primary B cells from cord blood	blood
20	chr1:59121400-59134800	Strong transcription	Placenta	Placenta
21	chr1:59121400-59145400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:59121400-59161000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:59121600-59130800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:59121600-59130800	Strong transcription	Osteobl	bone
25	chr1:59121600-59131400	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr1:59121600-59134200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:59121600-59139800	Weak transcription	Hela-S3	cervix
28	chr1:59121600-59141600	Strong transcription	NH-A	brain
29	chr1:59121600-59142200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:59121600-59143000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:59121600-59143000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:59121600-59147400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:59121600-59148400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:59121600-59150000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:59121600-59150000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:59121600-59150600	Strong transcription	Liver	Liver
37	chr1:59121600-59161200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:59121600-59161200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:59121800-59130800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:59121800-59134600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:59122200-59130600	Weak transcription	Colonic Mucosa	Colon
42	chr1:59122200-59153400	Weak transcription	Esophagus	oesophagus
43	chr1:59122400-59131400	Weak transcription	Fetal Intestine Small	intestine
44	chr1:59122400-59138400	Weak transcription	Lung	lung
45	chr1:59122400-59153200	Weak transcription	Gastric	stomach
46	chr1:59122400-59153200	Weak transcription	Pancreas	Pancrea
47	chr1:59122400-59155200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:59122400-59159400	Weak transcription	Right Ventricle	heart
49	chr1:59122800-59133400	Strong transcription	GM12878-XiMat	blood
50	chr1:59122800-59141800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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