Variant report

Variant	rs3969942
Chromosome Location	chr3:48555652-48555653
allele	A/G
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:
2	chr3:48553221..48555693-chr3:48556797..48558474,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1003649	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs10049154	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10470687	0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap]
rs12107418	0.83[GIH][hapmap]
rs13060933	0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs13062576	0.82[CHB][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13063312	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs13064619	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13070798	0.83[GIH][hapmap]
rs13091944	0.85[ASN][1000 genomes]
rs13094578	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]
rs13100178	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319635	0.81[ASN][1000 genomes]
rs13319651	0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs13324142	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs13434258	0.83[GIH][hapmap]
rs1459247	0.82[JPT][hapmap]
rs17080289	0.85[CHD][hapmap];0.83[GIH][hapmap]
rs2006871	0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs2276850	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs2276852	0.83[GIH][hapmap]
rs2286652	0.83[GIH][hapmap]
rs2310996	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs2854394	0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs28563843	0.86[ASN][1000 genomes]
rs28881595	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35562294	0.82[ASN][1000 genomes]
rs3755819	0.82[ASN][1000 genomes]
rs3821876	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs4075082	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442126	0.86[CHB][hapmap]
rs6442127	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765317	0.94[ASN][1000 genomes]
rs6781283	0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][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]
rs6792156	0.81[CHD][hapmap];0.83[GIH][hapmap]
rs6792525	0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs6806059	0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6809981	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740787	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs7428949	0.89[CHB][hapmap];1.00[ASN][1000 genomes]
rs7434077	0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs7434107	1.00[ASN][1000 genomes]
rs7623614	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631574	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs7640031	1.00[ASN][1000 genomes]
rs7644771	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs9810991	0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap]
rs9812200	0.83[GIH][hapmap]
rs9814951	0.85[GIH][hapmap]
rs9816942	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822677	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830581	0.84[CHD][hapmap];0.83[GIH][hapmap]
rs9835827	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835902	0.89[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836462	0.83[GIH][hapmap]
rs9837687	0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap]
rs9843316	0.85[CHD][hapmap];0.83[GIH][hapmap]
rs9848824	0.86[ASN][1000 genomes]
rs9849280	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9850102	0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[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	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862906	0.80[AMR][1000 genomes]
rs9864729	0.86[ASN][1000 genomes]
rs9869698	0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs9871180	0.80[CHD][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs9871608	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875911	1.00[GIH][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.85[AFR][1000 genomes]
rs9878950	0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs9881877	0.85[CHD][hapmap];0.83[GIH][hapmap];0.82[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.80[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:97 , 50 per page) page: 1 2

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	chr3:48543000-48556000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:48543000-48556400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:48543000-48556600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:48544000-48561000	Weak transcription	K562	blood
8	chr3:48545000-48559800	Weak transcription	Fetal Intestine Large	intestine
9	chr3:48545200-48558400	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:48545200-48558600	Weak transcription	NHLF	lung
11	chr3:48545200-48572400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:48545400-48556000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:48545400-48556000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:48545400-48556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:48545400-48556400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:48545400-48556600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:48545400-48556800	Weak transcription	Brain Substantia Nigra	brain
18	chr3:48545400-48558400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:48545400-48558800	Weak transcription	Gastric	stomach
20	chr3:48545400-48565400	Weak transcription	Pancreas	Pancrea
21	chr3:48545400-48572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:48545400-48572600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:48545600-48555800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:48545600-48556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:48545600-48562600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:48545600-48570600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:48545600-48571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:48545600-48572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:48547400-48556200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:48547400-48556200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:48547400-48556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:48547400-48556600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:48547400-48556600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:48547400-48559000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:48547400-48562000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:48547600-48556000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:48550000-48555800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:48550400-48557800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:48551600-48558200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:48552000-48556200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:48552600-48555800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:48552600-48556000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:48552600-48556000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:48552600-48557400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr3:48552600-48557600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:48552600-48558000	Enhancers	Primary T cells fromperipheralblood	blood
48	chr3:48552800-48557600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:48552800-48572600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:48553000-48557600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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