Variant report

Variant	rs7041487
Chromosome Location	chr9:116777878-116777879
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116773482..116775850-chr9:116777082..116779157,3	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1006540	0.91[CHB][hapmap]
rs1006541	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1008138	0.87[CHB][hapmap]
rs10441747	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10513224	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10739398	0.95[CHB][hapmap]
rs10739399	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759668	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10759669	0.87[CHB][hapmap]
rs10759670	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10759671	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs10759672	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10759673	0.81[ASN][1000 genomes]
rs10759674	0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10759676	0.95[CHB][hapmap]
rs10759677	1.00[CEU][hapmap];0.85[YRI][hapmap];0.99[EUR][1000 genomes]
rs10759678	0.87[CEU][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes]
rs10817545	0.87[CHB][hapmap]
rs10817546	0.87[CHB][hapmap]
rs10817547	0.86[CHB][hapmap]
rs10817548	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10817549	0.81[ASN][1000 genomes]
rs10817553	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817555	0.95[CHB][hapmap]
rs10817556	0.95[ASN][1000 genomes]
rs10817557	0.86[CEU][hapmap];0.87[JPT][hapmap];0.96[EUR][1000 genomes]
rs10982029	0.95[CHB][hapmap]
rs10982031	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs10982032	0.95[ASN][1000 genomes]
rs10982042	0.86[CHB][hapmap]
rs11788583	0.91[CHB][hapmap]
rs11788633	0.95[CHB][hapmap]
rs11788661	0.95[CHB][hapmap]
rs11791155	0.86[CHB][hapmap]
rs11791230	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs12551686	0.95[CHB][hapmap]
rs12682865	0.86[CHB][hapmap]
rs12686727	0.95[CHB][hapmap]
rs13298270	0.95[CHB][hapmap]
rs1330171	0.86[CHB][hapmap]
rs1408112	0.91[CHB][hapmap]
rs1408113	0.91[CHB][hapmap]
rs1408114	0.91[CHB][hapmap]
rs1408115	0.81[CHB][hapmap]
rs1535762	0.82[CHB][hapmap]
rs1535763	0.82[CHB][hapmap]
rs1535764	0.91[CHB][hapmap]
rs1590367	0.82[CHB][hapmap]
rs1835731	0.97[EUR][1000 genomes]
rs1853546	0.87[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs1886129	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1928699	0.87[CHB][hapmap]
rs1965753	0.81[CHB][hapmap]
rs1991706	0.87[CEU][hapmap];0.96[EUR][1000 genomes]
rs2078305	0.81[CHB][hapmap]
rs2116406	0.87[CEU][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes]
rs2116407	0.91[CHB][hapmap]
rs2163575	0.96[EUR][1000 genomes]
rs2418262	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2418263	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs3748183	0.95[CHB][hapmap]
rs3860174	0.86[CHB][hapmap]
rs4497041	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs4641141	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs4978561	0.91[CHB][hapmap]
rs4978562	0.95[CHB][hapmap]
rs4979310	0.87[CHB][hapmap]
rs4979311	0.86[CHB][hapmap]
rs4979316	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4979317	0.91[CHB][hapmap]
rs4979318	0.91[CHB][hapmap]
rs4979319	1.00[CHB][hapmap]
rs4979320	0.95[CHB][hapmap]
rs4979321	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4979322	0.95[CHB][hapmap]
rs4979323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4979324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979325	0.87[CEU][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes]
rs4979326	0.95[CHB][hapmap]
rs4979327	0.95[CHB][hapmap]
rs4979328	0.81[JPT][hapmap]
rs4979331	0.82[CHB][hapmap]
rs6478050	0.91[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7020561	0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs7023499	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7026668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7028504	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7031814	0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7032124	0.81[ASN][1000 genomes]
rs7032729	0.86[CHB][hapmap]
rs7034528	0.91[CHB][hapmap]
rs7036201	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs7040742	0.87[CEU][hapmap];0.97[EUR][1000 genomes]
rs7041524	0.95[CHB][hapmap]
rs7042021	1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs7042081	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850217	0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7858120	0.95[CHB][hapmap]
rs7863348	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs7863469	0.81[ASN][1000 genomes]
rs814701	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs860082	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs9332459	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs942286	0.91[CHB][hapmap]
rs942287	0.90[CHB][hapmap]
rs9695257	0.87[CHB][hapmap]
rs9696305	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv521361	chr9:116774010-116780992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:116736400-116783000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:116756800-116779000	Weak transcription	Esophagus	oesophagus
4	chr9:116756800-116783800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:116757000-116779600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:116757000-116779800	Weak transcription	Colonic Mucosa	Colon
7	chr9:116757000-116783400	Weak transcription	Small Intestine	intestine
8	chr9:116762200-116780400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:116764600-116797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:116765000-116783200	Weak transcription	NHEK	skin
11	chr9:116765800-116784400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:116766000-116784800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:116766000-116792600	Weak transcription	Stomach Mucosa	stomach
14	chr9:116766000-116798000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:116766200-116799000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:116766600-116782400	Strong transcription	A549	lung
17	chr9:116766600-116811200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:116767000-116780400	Weak transcription	Brain Angular Gyrus	brain
19	chr9:116767200-116779000	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:116767200-116779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:116767200-116785800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:116768400-116794600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:116768800-116778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:116768800-116784800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:116769200-116779000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:116769400-116778000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:116769400-116780200	Weak transcription	Thymus	Thymus
28	chr9:116769400-116790400	Weak transcription	Right Ventricle	heart
29	chr9:116770400-116779800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:116771000-116779000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:116771200-116779200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:116771400-116779200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:116771600-116778400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:116771800-116779000	Weak transcription	Gastric	stomach
35	chr9:116772000-116779000	Weak transcription	Spleen	Spleen
36	chr9:116772400-116779000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:116773600-116809200	Weak transcription	Fetal Heart	heart
38	chr9:116774000-116779000	Weak transcription	Brain Germinal Matrix	brain
39	chr9:116774000-116779000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:116774000-116780400	Weak transcription	Brain Substantia Nigra	brain
41	chr9:116774000-116791200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:116774000-116791200	Weak transcription	Fetal Brain Male	brain
43	chr9:116774200-116778000	Weak transcription	NHDF-Ad	bronchial
44	chr9:116774200-116778400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:116774200-116778400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:116774200-116778600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr9:116774200-116778800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:116774200-116779000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr9:116774200-116779000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr9:116774200-116783800	Weak transcription	HMEC	breast

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