Variant report

Variant	rs2064374
Chromosome Location	chr1:59160885-59160886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:59160837-59161260	MCF-7	breast:	n/a	chr1:59161058-59161067 chr1:59161057-59161067 chr1:59161057-59161068 chr1:59161057-59161066 chr1:59161056-59161069 chr1:59161057-59161068 chr1:59161058-59161065 chr1:59161056-59161071 chr1:59161057-59161068 chr1:59161056-59161069

No.	Distal block	Cell Line	Cell type
1	chr1:59124310..59126934-chr1:59160369..59163254,2	K562	blood:
2	chr1:59160810..59163384-chr1:59173119..59175841,2	K562	blood:
3	chr1:58980558..58982758-chr1:59159727..59161929,2	K562	blood:

Variant related genes	Relation type
MYSM1	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10158502	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10159308	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10789070	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889110	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10889111	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889112	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889113	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11207286	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207289	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11207292	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207293	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207298	0.94[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11803186	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12076049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12076717	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12082097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12092121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12097333	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12097517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12139511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12741968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12755615	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1323280	0.82[EUR][1000 genomes]
rs2029648	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064371	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2206765	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2223698	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs232775	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs232776	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232781	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232791	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs232851	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232861	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232869	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs232872	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406931	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2746081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2746082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2811893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4506484	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4912370	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4912373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506078	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527445	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs554318	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs579110	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs584284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587836	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656037	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656370	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6656503	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6658186	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661709	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6664782	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6668605	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6677560	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680626	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6680750	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6686043	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6701772	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2064374	MYSM1	cis	cerebellum	SCAN
rs2064374	MYSM1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59118200-59163400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:59119800-59162200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:59119800-59163200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:59121000-59161200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:59121400-59161000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:59121600-59161200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:59121600-59161200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:59123800-59161800	Strong transcription	Dnd41	blood
9	chr1:59125000-59162200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:59125600-59161200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr1:59129200-59161000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr1:59131200-59161000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:59131200-59161000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:59139600-59162800	Weak transcription	Fetal Brain Male	brain
15	chr1:59139800-59162000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:59144600-59161800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:59146600-59163200	Strong transcription	Osteobl	bone
18	chr1:59148000-59161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:59148000-59164000	Weak transcription	A549	lung
20	chr1:59148200-59164400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:59149200-59161000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:59151000-59163200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:59151400-59161000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:59151400-59161200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:59151400-59161400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:59151800-59164400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:59152000-59161000	Weak transcription	Brain Substantia Nigra	brain
28	chr1:59152200-59163200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:59153000-59161200	Strong transcription	HUVEC	blood vessel
30	chr1:59153200-59161200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:59153400-59162600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:59153600-59161800	Weak transcription	Fetal Heart	heart
33	chr1:59153600-59164400	Weak transcription	Right Atrium	heart
34	chr1:59153600-59164800	Weak transcription	Esophagus	oesophagus
35	chr1:59153800-59162000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:59153800-59164000	Weak transcription	Gastric	stomach
37	chr1:59153800-59165000	Weak transcription	Pancreas	Pancrea
38	chr1:59154200-59161000	Strong transcription	Liver	Liver
39	chr1:59154400-59161400	Strong transcription	Placenta	Placenta
40	chr1:59154600-59161000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:59154600-59161200	Strong transcription	Fetal Intestine Large	intestine
42	chr1:59154600-59161200	Strong transcription	Fetal Thymus	thymus
43	chr1:59154800-59161200	Strong transcription	HepG2	liver
44	chr1:59155200-59164400	Weak transcription	Hela-S3	cervix
45	chr1:59155200-59164600	Weak transcription	HSMMtube	muscle
46	chr1:59155400-59161000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:59155400-59161800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:59155400-59162600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:59155600-59161000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:59155600-59161200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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