Variant report

Variant	rs9647412
Chromosome Location	chr3:196278366-196278367
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	chr3:196277670..196280176-chr3:196286721..196289590,3	MCF-7	breast:
2	chr3:196277565..196279169-chr3:196291112..196294085,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11185544	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[ASN][1000 genomes]
rs11185545	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1124996	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11706197	0.89[ASN][1000 genomes]
rs11707537	0.84[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11711594	0.84[AMR][1000 genomes]
rs11711952	0.84[ASN][1000 genomes]
rs11714694	0.84[ASN][1000 genomes]
rs11920455	0.81[ASN][1000 genomes]
rs12495687	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1355533	1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs2054748	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054749	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054750	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086891	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2137193	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2341334	0.81[ASN][1000 genomes]
rs2341399	0.80[CEU][hapmap];0.87[CHD][hapmap];0.85[TSI][hapmap]
rs28479172	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34292861	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3964310	0.84[ASN][1000 genomes]
rs4488870	0.84[ASN][1000 genomes]
rs4916433	0.98[EUR][1000 genomes]
rs56144237	0.81[ASN][1000 genomes]
rs60668021	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583317	0.85[AMR][1000 genomes]
rs6583318	0.85[AMR][1000 genomes]
rs66588136	0.83[AMR][1000 genomes]
rs6765975	0.84[ASN][1000 genomes]
rs6775806	0.84[ASN][1000 genomes]
rs6778889	0.87[CHD][hapmap]
rs6780633	0.84[ASN][1000 genomes]
rs6780856	0.84[ASN][1000 genomes]
rs6799697	0.82[ASN][1000 genomes]
rs73219653	0.84[ASN][1000 genomes]
rs73219654	0.84[ASN][1000 genomes]
rs73219660	0.84[ASN][1000 genomes]
rs7615547	0.84[ASN][1000 genomes]
rs7619117	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7621684	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7623111	0.84[ASN][1000 genomes]
rs7626039	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7629990	0.82[CHB][hapmap]
rs7638562	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647413	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811428	0.84[ASN][1000 genomes]
rs9813420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817377	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818507	0.84[ASN][1000 genomes]
rs9828786	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9831225	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839347	0.84[ASN][1000 genomes]
rs9839388	0.84[CEU][hapmap]
rs9840938	0.84[ASN][1000 genomes]
rs9843607	0.98[EUR][1000 genomes]
rs9848622	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs9849530	0.84[ASN][1000 genomes]
rs9853777	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9868492	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9880563	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv2763750	chr3:196242261-196278366	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196272600-196287400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:196272600-196288000	Weak transcription	K562	blood
3	chr3:196274200-196286800	Weak transcription	Liver	Liver
4	chr3:196276400-196280000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:196276800-196293800	Weak transcription	HepG2	liver
6	chr3:196277000-196285800	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:196277200-196280600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:196277200-196280800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:196277400-196285400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:196277600-196281200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:196277600-196284800	Weak transcription	Thymus	Thymus
12	chr3:196277600-196287800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:196277600-196290200	Weak transcription	NH-A	brain
14	chr3:196277600-196294200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:196277800-196280000	Weak transcription	Primary B cells from cord blood	blood
16	chr3:196277800-196280600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:196277800-196281400	Weak transcription	Fetal Thymus	thymus
18	chr3:196277800-196285800	Weak transcription	Aorta	Aorta
19	chr3:196277800-196287600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:196277800-196287600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:196277800-196287800	Weak transcription	Fetal Brain Female	brain
22	chr3:196277800-196293600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:196278000-196281200	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:196278000-196286000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:196278000-196286400	Weak transcription	Fetal Stomach	stomach
26	chr3:196278000-196287600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:196278000-196287600	Weak transcription	HSMMtube	muscle
28	chr3:196278000-196294400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:196278200-196287400	Weak transcription	NHDF-Ad	bronchial
30	chr3:196278200-196288200	Weak transcription	Rectal Smooth Muscle	rectum

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