Variant report

Variant	rs179798
Chromosome Location	chr1:59050556-59050557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59047843..59052771-chr1:59082760..59087529,8	MCF-7	breast:
2	chr1:59049156..59051350-chr1:59080976..59082563,2	MCF-7	breast:
3	chr1:59048457..59052619-chr1:59081708..59087602,8	MCF-7	breast:
4	chr1:59049910..59054215-chr1:59054903..59060265,8	MCF-7	breast:
5	chr1:59049755..59053628-chr1:59060314..59062387,4	MCF-7	breast:
6	chr1:59049811..59051312-chr1:59248040..59250365,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10489816	0.92[CEU][hapmap]
rs11207256	0.92[CEU][hapmap]
rs11799408	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11799786	0.86[CEU][hapmap]
rs11800241	0.85[CEU][hapmap]
rs11801938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11802520	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs11805031	0.86[CEU][hapmap]
rs11805701	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11805835	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11807197	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11808437	0.86[CEU][hapmap]
rs11808438	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11808738	0.86[CEU][hapmap]
rs11809508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs14008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1503646	0.86[CEU][hapmap]
rs1503647	0.86[CEU][hapmap]
rs1503648	0.86[CEU][hapmap]
rs1627332	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs17096876	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117574	0.92[CEU][hapmap]
rs17117627	0.92[CEU][hapmap]
rs17117643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17117647	0.86[CEU][hapmap]
rs17117650	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117654	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117666	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117678	0.92[CEU][hapmap]
rs17117681	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117688	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117699	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117714	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117717	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117720	0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117732	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17117747	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs17117850	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17447078	0.86[CEU][hapmap]
rs17498811	0.84[CEU][hapmap]
rs17506467	0.86[CEU][hapmap]
rs1775001	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs1847351	0.86[CEU][hapmap]
rs1891435	0.92[CEU][hapmap]
rs2268943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2271005	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs232835	0.96[ASN][1000 genomes]
rs232840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs232843	0.87[EUR][1000 genomes]
rs232845	0.87[EUR][1000 genomes]
rs232846	0.87[EUR][1000 genomes]
rs338234	0.92[CEU][hapmap]
rs35075952	0.87[EUR][1000 genomes]
rs41311174	0.87[EUR][1000 genomes]
rs488606	0.84[CEU][hapmap]
rs4912196	0.86[CEU][hapmap]
rs4912340	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4912341	0.86[CEU][hapmap]
rs4912345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4912346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4912347	0.92[CEU][hapmap]
rs492988	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs511687	0.87[EUR][1000 genomes]
rs512462	0.87[EUR][1000 genomes]
rs518070	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs530095	0.92[CEU][hapmap]
rs532134	0.86[CEU][hapmap]
rs542727	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs544596	0.87[EUR][1000 genomes]
rs546271	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs546358	0.87[EUR][1000 genomes]
rs548275	0.87[EUR][1000 genomes]
rs56109164	0.90[EUR][1000 genomes]
rs564252	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs565008	0.86[EUR][1000 genomes]
rs565617	0.87[EUR][1000 genomes]
rs565954	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs567787	0.84[EUR][1000 genomes]
rs573135	0.87[EUR][1000 genomes]
rs58370911	0.85[ASN][1000 genomes]
rs586847	0.87[EUR][1000 genomes]
rs59493428	0.89[ASN][1000 genomes]
rs594973	0.87[EUR][1000 genomes]
rs595909	0.87[EUR][1000 genomes]
rs60008712	0.89[ASN][1000 genomes]
rs60179866	0.88[ASN][1000 genomes]
rs60614132	0.85[ASN][1000 genomes]
rs61629658	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61779267	0.87[EUR][1000 genomes]
rs61779289	0.87[EUR][1000 genomes]
rs61779290	0.87[EUR][1000 genomes]
rs61779294	0.84[EUR][1000 genomes]
rs61781815	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61781821	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61781822	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61781823	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61781824	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs621754	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs627633	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs628623	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs635775	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs641929	0.87[EUR][1000 genomes]
rs654299	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs657202	0.85[EUR][1000 genomes]
rs657711	0.87[EUR][1000 genomes]
rs6587829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs664570	0.87[EUR][1000 genomes]
rs6683669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6684437	0.93[CEU][hapmap]
rs6684553	0.92[CEU][hapmap]
rs6686976	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6694699	0.86[CEU][hapmap]
rs6698355	0.92[CEU][hapmap]
rs671830	0.86[EUR][1000 genomes]
rs672859	0.86[EUR][1000 genomes]
rs673276	0.86[EUR][1000 genomes]
rs725907	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72672292	0.99[ASN][1000 genomes]
rs729084	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7355030	0.92[CEU][hapmap]
rs7511732	0.86[CEU][hapmap]
rs7513876	0.84[CEU][hapmap]
rs7514159	0.85[CEU][hapmap]
rs7519465	0.87[EUR][1000 genomes]
rs7535313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7537470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7548097	0.92[CEU][hapmap]
rs9583	0.92[CEU][hapmap];0.87[EUR][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
rs179798	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59049000-59050800	Enhancers	Placenta	Placenta
2	chr1:59049000-59050800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr1:59049000-59051000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:59049000-59051000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr1:59049000-59051200	Enhancers	Lung	lung
6	chr1:59049000-59051200	Enhancers	Stomach Mucosa	stomach
7	chr1:59049000-59051600	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:59049000-59051600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:59049000-59052000	Enhancers	HSMMtube	muscle
10	chr1:59049000-59052200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:59049000-59052400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:59049000-59052400	Enhancers	Fetal Lung	lung
13	chr1:59049000-59052800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:59049000-59052800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:59049200-59050600	Enhancers	Fetal Muscle Leg	muscle
16	chr1:59049200-59050600	Enhancers	HepG2	liver
17	chr1:59049200-59050800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:59049200-59051200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:59049200-59051200	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:59049200-59051400	Enhancers	K562	blood
21	chr1:59049200-59051600	Enhancers	Adipose Nuclei	Adipose
22	chr1:59049200-59052400	Enhancers	Aorta	Aorta
23	chr1:59049200-59052400	Enhancers	NHDF-Ad	bronchial
24	chr1:59049200-59052800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:59049200-59052800	Enhancers	Esophagus	oesophagus
26	chr1:59049400-59050800	Weak transcription	Spleen	Spleen
27	chr1:59049400-59051000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:59049400-59051400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:59049400-59057800	Weak transcription	Gastric	stomach
30	chr1:59049600-59051200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr1:59049600-59051200	Enhancers	Colon Smooth Muscle	Colon
32	chr1:59049800-59050600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:59049800-59050600	Enhancers	Right Atrium	heart
34	chr1:59049800-59051000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr1:59049800-59051200	Enhancers	Stomach Smooth Muscle	stomach
36	chr1:59049800-59051600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:59049800-59052800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:59049800-59052800	Enhancers	Ovary	ovary
39	chr1:59050000-59050600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr1:59050000-59050600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr1:59050000-59050600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:59050000-59050600	Flanking Active TSS	A549	lung
43	chr1:59050000-59051800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:59050200-59050800	Enhancers	Duodenum Mucosa	Duodenum
45	chr1:59050200-59051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:59050200-59052400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:59050200-59052800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:59050200-59052800	Enhancers	HMEC	breast
49	chr1:59050200-59052800	Enhancers	HSMM	muscle
50	chr1:59050200-59053000	Enhancers	HUVEC	blood vessel

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