Variant report

Variant	rs13094578
Chromosome Location	chr3:48556231-48556232
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48538484..48541127-chr3:48554924..48556853,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10049154	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10470687	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs13060933	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13064619	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13069724	0.80[YRI][hapmap]
rs13091944	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs13100178	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319635	0.81[ASN][1000 genomes]
rs13319651	0.81[ASN][1000 genomes]
rs1459247	0.82[JPT][hapmap]
rs2006871	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs2302295	0.82[JPT][hapmap]
rs28563843	0.86[ASN][1000 genomes]
rs28881595	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35562294	0.82[ASN][1000 genomes]
rs3755819	0.82[ASN][1000 genomes]
rs3969942	0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075082	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442126	1.00[CHB][hapmap]
rs6442127	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765317	0.94[ASN][1000 genomes]
rs6773261	0.82[JPT][hapmap]
rs6781283	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs6785845	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786424	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6792525	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs6806059	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6809981	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7428949	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7434077	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7434107	1.00[ASN][1000 genomes]
rs7620853	0.82[JPT][hapmap]
rs7623614	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640031	1.00[ASN][1000 genomes]
rs7644771	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs9810991	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs9816942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821797	0.82[JPT][hapmap]
rs9822677	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835827	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837687	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs9848824	0.86[ASN][1000 genomes]
rs9849280	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9850102	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9851743	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862906	0.90[AMR][1000 genomes]
rs9864729	0.86[ASN][1000 genomes]
rs9869698	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs9871608	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875911	0.85[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9878950	0.81[ASN][1000 genomes]
rs9881877	0.82[ASN][1000 genomes]
rs9882962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48542800-48558200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:48542800-48562800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:48542800-48569800	Weak transcription	Right Atrium	heart
4	chr3:48543000-48556400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:48543000-48556600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:48544000-48561000	Weak transcription	K562	blood
7	chr3:48545000-48559800	Weak transcription	Fetal Intestine Large	intestine
8	chr3:48545200-48558400	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:48545200-48558600	Weak transcription	NHLF	lung
10	chr3:48545200-48572400	Weak transcription	Brain Angular Gyrus	brain
11	chr3:48545400-48556400	Weak transcription	Brain Anterior Caudate	brain
12	chr3:48545400-48556600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:48545400-48556800	Weak transcription	Brain Substantia Nigra	brain
14	chr3:48545400-48558400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:48545400-48558800	Weak transcription	Gastric	stomach
16	chr3:48545400-48565400	Weak transcription	Pancreas	Pancrea
17	chr3:48545400-48572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:48545400-48572600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:48545600-48562600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:48545600-48570600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:48545600-48571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:48545600-48572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:48547400-48556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:48547400-48556600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:48547400-48556600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:48547400-48559000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:48547400-48562000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:48550400-48557800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:48551600-48558200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:48552600-48557400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr3:48552600-48557600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:48552600-48558000	Enhancers	Primary T cells fromperipheralblood	blood
34	chr3:48552800-48557600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:48552800-48572600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:48553000-48557600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr3:48553200-48556600	Weak transcription	GM12878-XiMat	blood
38	chr3:48553200-48558400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:48553400-48558400	Weak transcription	A549	lung
40	chr3:48553600-48559400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:48553600-48564000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:48554000-48557200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr3:48554000-48573000	Weak transcription	Right Ventricle	heart
44	chr3:48554200-48557200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:48554200-48557800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr3:48554200-48557800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:48554200-48559600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:48554200-48561000	Weak transcription	Lung	lung
49	chr3:48554200-48565000	Strong transcription	Fetal Intestine Small	intestine
50	chr3:48554200-48572600	Weak transcription	Rectal Mucosa Donor 31	rectum

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