Variant report

Variant	rs3936499
Chromosome Location	chr10:28580010-28580011
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	chr10:28542308..28543962-chr10:28578219..28580065,2	MCF-7	breast:
2	chr10:28564267..28567183-chr10:28578724..28581652,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10826441	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826442	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10826444	0.92[ASN][1000 genomes]
rs11006983	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11006986	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006987	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11006988	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11006992	0.87[CHB][hapmap];0.98[GIH][hapmap]
rs11006995	0.87[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap]
rs11007003	0.85[CEU][hapmap]
rs11007010	0.81[EUR][1000 genomes]
rs1148174	0.86[JPT][hapmap]
rs12218186	0.81[EUR][1000 genomes]
rs12219880	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12256403	0.86[JPT][hapmap]
rs12570446	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2124955	0.80[JPT][hapmap]
rs3842931	0.87[CHB][hapmap]
rs3843586	0.81[EUR][1000 genomes]
rs3936496	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3936497	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3939436	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7089787	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7895813	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7905490	0.86[JPT][hapmap]
rs7918097	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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

No data

Chromatin state (count:37 , 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	chr10:28571000-28580200	Weak transcription	Lung	lung
3	chr10:28571400-28584600	Weak transcription	Fetal Intestine Small	intestine
4	chr10:28571600-28580200	Weak transcription	Esophagus	oesophagus
5	chr10:28571600-28580200	Weak transcription	Left Ventricle	heart
6	chr10:28571600-28583800	Weak transcription	Fetal Muscle Leg	muscle
7	chr10:28571800-28580200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:28571800-28587800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:28572000-28580200	Weak transcription	Psoas Muscle	Psoas
10	chr10:28572000-28580400	Weak transcription	Aorta	Aorta
11	chr10:28572400-28582200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr10:28573600-28580200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr10:28573600-28581000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:28573600-28582600	Weak transcription	Primary T cells from cord blood	blood
15	chr10:28573600-28582600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr10:28573800-28581000	Weak transcription	Fetal Heart	heart
17	chr10:28573800-28587400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr10:28575600-28580200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:28575600-28580200	Weak transcription	Pancreas	Pancrea
20	chr10:28575800-28580200	Weak transcription	HSMMtube	muscle
21	chr10:28575800-28581000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:28575800-28582000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr10:28576400-28581000	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:28576400-28582200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr10:28577800-28585200	Weak transcription	Gastric	stomach
26	chr10:28578400-28583000	Weak transcription	HepG2	liver
27	chr10:28578600-28583800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr10:28578800-28582200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr10:28579000-28588400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr10:28579400-28585000	Weak transcription	Stomach Mucosa	stomach
31	chr10:28579600-28580400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:28580000-28580200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr10:28580000-28581000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr10:28580000-28581000	Enhancers	NH-A	brain
35	chr10:28580000-28581200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr10:28580000-28581800	Enhancers	HMEC	breast
37	chr10:28580000-28590400	Enhancers	Primary T helper cells PMA-I stimulated	--

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