Variant report

Variant	rs4979321
Chromosome Location	chr9:116769515-116769516
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	chr9:116768367..116772045-chr9:116772665..116776100,5	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1006540	0.86[CHB][hapmap]
rs1006541	0.86[CHB][hapmap]
rs1008138	0.82[CHB][hapmap]
rs10441747	0.86[CHB][hapmap]
rs10513224	0.86[CHB][hapmap]
rs10739398	0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10739399	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10759668	0.86[CHB][hapmap]
rs10759669	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10759670	0.86[CHB][hapmap]
rs10759671	0.86[CHB][hapmap]
rs10759672	0.86[CHB][hapmap]
rs10759674	0.90[CHB][hapmap]
rs10759675	0.88[ASN][1000 genomes]
rs10759676	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10759677	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10759678	0.86[CEU][hapmap];0.95[EUR][1000 genomes]
rs10817545	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10817546	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10817547	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10817548	0.90[CHB][hapmap]
rs10817552	0.91[ASN][1000 genomes]
rs10817553	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817555	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10817557	0.86[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs10982026	0.85[ASN][1000 genomes]
rs10982029	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs10982031	0.95[CHB][hapmap]
rs10982034	0.86[ASN][1000 genomes]
rs10982042	0.81[CHB][hapmap]
rs11788583	0.86[CHB][hapmap]
rs11788633	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs11788661	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs11788667	0.91[ASN][1000 genomes]
rs11791155	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs11791230	0.95[CHB][hapmap]
rs12551686	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12682865	0.91[CHB][hapmap]
rs12686226	0.85[CHB][hapmap]
rs12686727	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs13298270	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1330171	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1408112	0.86[CHB][hapmap]
rs1408113	0.86[CHB][hapmap]
rs1408114	0.86[CHB][hapmap]
rs1408115	0.86[CHB][hapmap]
rs1535762	0.86[CHB][hapmap]
rs1535763	0.86[CHB][hapmap]
rs1535764	0.86[CHB][hapmap]
rs1590367	0.86[CHB][hapmap]
rs1835731	0.95[EUR][1000 genomes]
rs1853546	0.98[GIH][hapmap];0.90[TSI][hapmap]
rs1886129	0.86[CHB][hapmap]
rs1928699	0.81[CHB][hapmap]
rs1965753	0.86[CHB][hapmap]
rs1991706	0.86[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs2078305	0.86[CHB][hapmap]
rs2116406	0.87[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs2116407	0.86[CHB][hapmap]
rs2163575	0.95[EUR][1000 genomes]
rs2418262	0.86[CHB][hapmap]
rs2418263	0.90[CHB][hapmap]
rs3748182	0.89[ASN][1000 genomes]
rs3748183	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs3860174	0.91[CHB][hapmap]
rs4497041	0.86[CHB][hapmap]
rs4641141	0.81[CHB][hapmap]
rs4978561	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4978562	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs4979310	0.91[CHB][hapmap]
rs4979311	0.91[CHB][hapmap]
rs4979316	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4979317	0.95[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs4979318	0.95[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs4979319	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs4979320	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4979322	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs4979323	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4979324	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4979325	0.87[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs4979326	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs4979327	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs4979331	0.86[CHB][hapmap]
rs6478050	0.86[CHB][hapmap]
rs7020561	0.91[CHB][hapmap]
rs7023499	0.91[CHB][hapmap]
rs7026668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7028504	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7031814	0.88[CHB][hapmap]
rs7032729	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs7034528	0.86[CHB][hapmap]
rs7036201	0.82[CHB][hapmap]
rs7040742	0.87[CEU][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs7041487	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7041524	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs7042021	0.95[CHB][hapmap]
rs7042081	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7850217	0.91[CHB][hapmap]
rs7858120	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs7863348	0.83[CHB][hapmap]
rs814701	0.86[CHB][hapmap]
rs860082	0.86[CHB][hapmap]
rs9332459	0.86[CHB][hapmap]
rs942286	0.95[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs942287	0.95[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs9695257	0.91[CHB][hapmap]
rs9696305	0.86[CHB][hapmap]

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	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4979321	SUSD1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116732200-116773400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:116736400-116783000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:116751000-116773400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:116756200-116773800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:116756400-116775600	Weak transcription	Primary B cells from cord blood	blood
7	chr9:116756800-116779000	Weak transcription	Esophagus	oesophagus
8	chr9:116756800-116783800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:116757000-116770200	Weak transcription	Aorta	Aorta
10	chr9:116757000-116773600	Weak transcription	HMEC	breast
11	chr9:116757000-116779600	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:116757000-116779800	Weak transcription	Colonic Mucosa	Colon
13	chr9:116757000-116783400	Weak transcription	Small Intestine	intestine
14	chr9:116757600-116772200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:116758400-116775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:116760000-116773400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:116760800-116771600	Strong transcription	NHLF	lung
18	chr9:116762200-116770800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:116762200-116772800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:116762200-116775400	Strong transcription	Liver	Liver
21	chr9:116762200-116780400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:116762400-116776800	Strong transcription	Fetal Intestine Large	intestine
23	chr9:116763800-116777000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:116764000-116772200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:116764400-116771000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:116764600-116797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:116765000-116783200	Weak transcription	NHEK	skin
28	chr9:116765600-116770800	Weak transcription	Spleen	Spleen
29	chr9:116765600-116773200	Weak transcription	Psoas Muscle	Psoas
30	chr9:116765800-116784400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:116766000-116773000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:116766000-116784800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:116766000-116792600	Weak transcription	Stomach Mucosa	stomach
34	chr9:116766000-116798000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:116766200-116775000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:116766200-116799000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:116766400-116774400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:116766600-116782400	Strong transcription	A549	lung
39	chr9:116766600-116811200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:116766800-116772000	Strong transcription	Ovary	ovary
41	chr9:116766800-116775000	Strong transcription	Fetal Lung	lung
42	chr9:116767000-116771400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:116767000-116772200	Strong transcription	HSMMtube	muscle
44	chr9:116767000-116774400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:116767000-116780400	Weak transcription	Brain Angular Gyrus	brain
46	chr9:116767200-116769600	Weak transcription	Lung	lung
47	chr9:116767200-116770600	Strong transcription	Osteobl	bone
48	chr9:116767200-116771400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:116767200-116772000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr9:116767200-116772400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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