Variant report

Variant	rs17117968
Chromosome Location	chr1:59116045-59116046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59037535..59044875-chr1:59111123..59123546,29	MCF-7	breast:
2	chr1:59083668..59085660-chr1:59115397..59118343,2	MCF-7	breast:
3	chr1:59110150..59112392-chr1:59115500..59117344,2	K562	blood:
4	chr1:59036598..59046417-chr1:59110760..59123309,33	MCF-7	breast:
5	chr1:59110479..59112753-chr1:59115412..59117195,2	MCF-7	breast:
6	chr1:59112305..59114468-chr1:59114733..59116288,2	MCF-7	breast:
7	chr1:59009441..59012454-chr1:59115499..59119409,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162600	Chromatin interaction
ENSG00000184292	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10489540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207278	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207284	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11207297	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11207299	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12062727	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12070703	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12073211	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12078684	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12080369	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12082192	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12092264	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12562490	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12737926	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12742701	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1323281	0.85[TSI][hapmap]
rs17118041	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17118097	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961787	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2760480	0.83[TSI][hapmap]
rs2811856	0.82[CEU][hapmap]
rs2897558	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35180093	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4244016	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4414067	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4483434	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4553223	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4612650	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4912361	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4912364	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4912365	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4912366	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4912371	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4912375	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55677434	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55892958	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56398740	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61292499	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6659809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6664796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673162	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682078	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17117968	MYSM1	cis	parietal	SCAN
rs17117968	INADL	cis	parietal	SCAN
rs17117968	PCSK9	cis	parietal	SCAN
rs17117968	OMA1	cis	cerebellum	SCAN
rs17117968	MYSM1	cis	cerebellum	SCAN
rs17117968	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59096000-59121600	Weak transcription	HUVEC	blood vessel
2	chr1:59096600-59121600	Weak transcription	Gastric	stomach
3	chr1:59102000-59130400	Weak transcription	Aorta	Aorta
4	chr1:59108200-59130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:59108600-59121600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:59109000-59121600	Weak transcription	HepG2	liver
7	chr1:59109400-59121600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:59109600-59117800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:59110400-59121600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:59110400-59123600	Weak transcription	HSMMtube	muscle
11	chr1:59110600-59119200	Weak transcription	Placenta	Placenta
12	chr1:59110800-59125200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:59111600-59118200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:59112400-59121600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:59112600-59116200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:59112800-59125600	Weak transcription	NHLF	lung
17	chr1:59114200-59117600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:59114400-59116200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:59114400-59121600	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:59114400-59130200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:59114600-59116600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:59114600-59116600	Weak transcription	Dnd41	blood
23	chr1:59114600-59121600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:59114800-59116200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:59115000-59117600	Weak transcription	HSMM	muscle
26	chr1:59115000-59122800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:59115000-59132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:59115200-59119200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:59115200-59121600	Weak transcription	Primary T cells from cord blood	blood
30	chr1:59115400-59116200	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr1:59115400-59116400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr1:59115400-59116600	Weak transcription	K562	blood
33	chr1:59115400-59118000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:59115400-59118000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:59115400-59121400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:59115400-59121600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:59115400-59121600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:59115400-59123800	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:59115600-59116200	Weak transcription	Fetal Intestine Large	intestine
40	chr1:59115600-59116400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:59115600-59116400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:59115600-59116400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:59115600-59116600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:59115600-59117800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:59115600-59117800	Weak transcription	Brain Substantia Nigra	brain
46	chr1:59115600-59121600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:59115600-59121600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:59115600-59121600	Weak transcription	Thymus	Thymus
49	chr1:59115600-59121800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:59115600-59123000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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