Variant report

Variant	rs17118103
Chromosome Location	chr1:59148118-59148119
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11207290	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207291	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11576713	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12123717	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12139211	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144224	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12405774	0.92[JPT][hapmap]
rs12409869	0.92[JPT][hapmap]
rs12732648	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12746851	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492718	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1565662	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17117956	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17118106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961788	0.91[ASN][1000 genomes]
rs232777	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232780	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232782	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232785	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232786	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232787	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232789	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232792	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232793	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232794	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232795	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232852	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232854	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232855	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232856	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232858	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232860	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232864	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232865	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232866	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232870	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232874	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs232881	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232882	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232884	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232885	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232887	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232888	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232889	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232890	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232891	0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs232892	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232895	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232896	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232897	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232898	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs232899	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs232900	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs232903	0.96[ASN][1000 genomes]
rs23588	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34941709	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35091401	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4912202	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4912362	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4912368	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs516957	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587835	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587837	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664947	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700413	0.93[EUR][1000 genomes];0.98[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
rs17118103	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	chr1:59116000-59151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:59118200-59163400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:59119800-59155000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:59119800-59162200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:59119800-59163200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:59120000-59153400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:59120200-59149400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:59121000-59161200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:59121400-59161000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:59121600-59148400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:59121600-59150000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr1:59121600-59150000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:59121600-59150600	Strong transcription	Liver	Liver
14	chr1:59121600-59161200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:59121600-59161200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:59122200-59153400	Weak transcription	Esophagus	oesophagus
17	chr1:59122400-59153200	Weak transcription	Gastric	stomach
18	chr1:59122400-59153200	Weak transcription	Pancreas	Pancrea
19	chr1:59122400-59155200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:59122400-59159400	Weak transcription	Right Ventricle	heart
21	chr1:59123400-59153800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:59123800-59161800	Strong transcription	Dnd41	blood
23	chr1:59124000-59156600	Weak transcription	Spleen	Spleen
24	chr1:59125000-59162200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:59125200-59150000	Strong transcription	Fetal Thymus	thymus
26	chr1:59125600-59161200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:59126200-59153400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:59126800-59149800	Strong transcription	Fetal Intestine Large	intestine
29	chr1:59129200-59161000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:59130200-59150200	Weak transcription	Stomach Mucosa	stomach
31	chr1:59131200-59161000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:59131200-59161000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:59131600-59153200	Weak transcription	Aorta	Aorta
34	chr1:59135600-59150000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:59135600-59152000	Strong transcription	Placenta	Placenta
36	chr1:59136800-59152200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:59137000-59151200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:59137200-59155400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:59138800-59151400	Weak transcription	Ovary	ovary
40	chr1:59139400-59151400	Weak transcription	Brain Angular Gyrus	brain
41	chr1:59139400-59156200	Weak transcription	Psoas Muscle	Psoas
42	chr1:59139600-59151200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:59139600-59162800	Weak transcription	Fetal Brain Male	brain
44	chr1:59139800-59156200	Weak transcription	Lung	lung
45	chr1:59139800-59159000	Weak transcription	Small Intestine	intestine
46	chr1:59139800-59162000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:59140200-59158800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:59140400-59157800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:59140600-59151600	Weak transcription	Fetal Intestine Small	intestine
50	chr1:59141200-59156200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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