Variant report

Variant	rs3939436
Chromosome Location	chr10:28577449-28577450
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	chr10:28571543..28573303-chr10:28575111..28577967,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10826441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826442	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10826444	0.93[ASN][1000 genomes]
rs11006983	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11006986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006987	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11006988	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11007010	0.81[EUR][1000 genomes]
rs12218186	0.81[EUR][1000 genomes]
rs12219880	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12570446	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3843586	0.81[EUR][1000 genomes]
rs3936496	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3936497	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3936499	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7089787	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7895813	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7918097	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1040916	chr10:28558982-28579141	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
6	nsv437663	chr10:28562647-28585496	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1039546	chr10:28563995-28579141	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
8	nsv515548	chr10:28564732-28579969	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28550400-28582600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr10:28569000-28578400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr10:28571000-28580200	Weak transcription	Lung	lung
4	chr10:28571400-28578200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr10:28571400-28584600	Weak transcription	Fetal Intestine Small	intestine
6	chr10:28571600-28580200	Weak transcription	Esophagus	oesophagus
7	chr10:28571600-28580200	Weak transcription	Left Ventricle	heart
8	chr10:28571600-28583800	Weak transcription	Fetal Muscle Leg	muscle
9	chr10:28571800-28580200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:28571800-28587800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:28572000-28580200	Weak transcription	Psoas Muscle	Psoas
12	chr10:28572000-28580400	Weak transcription	Aorta	Aorta
13	chr10:28572200-28577600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr10:28572400-28582200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr10:28573600-28580200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr10:28573600-28581000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr10:28573600-28582600	Weak transcription	Primary T cells from cord blood	blood
18	chr10:28573600-28582600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr10:28573800-28581000	Weak transcription	Fetal Heart	heart
20	chr10:28573800-28587400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr10:28574000-28580000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr10:28574400-28577600	Weak transcription	HepG2	liver
23	chr10:28575600-28580200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:28575600-28580200	Weak transcription	Pancreas	Pancrea
25	chr10:28575800-28578600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr10:28575800-28580200	Weak transcription	HSMMtube	muscle
27	chr10:28575800-28581000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:28575800-28582000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr10:28576400-28580000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr10:28576400-28581000	Weak transcription	Colon Smooth Muscle	Colon
31	chr10:28576400-28582200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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