Variant report

Variant	rs10742827
Chromosome Location	chr11:48102350-48102351
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	chr11:48101649..48104254-chr11:48106713..48109745,3	MCF-7	breast:
2	chr11:48097619..48099123-chr11:48100995..48103478,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1039484	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1039485	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734561	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10742826	0.87[ASN][1000 genomes]
rs10769310	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769311	0.90[ASN][1000 genomes]
rs10769312	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs10769313	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769314	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769315	0.90[JPT][hapmap]
rs10838798	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10838800	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs10838801	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039513	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113480	0.86[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11601310	0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1472681	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1681630	0.80[GIH][hapmap]
rs1967211	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2904315	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4256933	0.92[ASN][1000 genomes]
rs4298856	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4412719	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508163	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6485806	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6485807	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118665	0.88[ASN][1000 genomes]
rs7122335	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7130876	0.81[JPT][hapmap]
rs7395231	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7396592	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7479361	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7934659	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
15	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
16	nsv897329	chr11:48052676-48319974	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1048554	chr11:48062861-48388686	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
18	nsv1038210	chr11:48068862-48388686	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
19	nsv1052076	chr11:48077864-48702549	ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
20	nsv1053528	chr11:48086151-48125731	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
21	nsv869354	chr11:48088580-48783113	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
22	nsv1045734	chr11:48089315-48893207	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
23	nsv1036541	chr11:48091589-48116032	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48079200-48102800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:48086000-48109200	Weak transcription	Fetal Intestine Large	intestine
3	chr11:48086200-48114400	Weak transcription	Hela-S3	cervix
4	chr11:48086800-48102800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:48089000-48105800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:48089200-48108000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:48089400-48102400	Weak transcription	HSMM	muscle
8	chr11:48090400-48103000	Weak transcription	Thymus	Thymus
9	chr11:48092400-48109400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:48094000-48103600	Weak transcription	Small Intestine	intestine
11	chr11:48095200-48114200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:48096400-48111200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr11:48096600-48102800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:48097200-48109800	Weak transcription	Colonic Mucosa	Colon
15	chr11:48097600-48109600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:48097600-48110000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:48099000-48102600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:48099000-48102800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:48099200-48102800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:48099200-48103000	Enhancers	Fetal Brain Male	brain
21	chr11:48099200-48104600	Enhancers	Brain Hippocampus Middle	brain
22	chr11:48099200-48105800	Weak transcription	Fetal Intestine Small	intestine
23	chr11:48099600-48103000	Weak transcription	HepG2	liver
24	chr11:48099800-48104000	Enhancers	Brain Angular Gyrus	brain
25	chr11:48100000-48103600	Enhancers	Brain Substantia Nigra	brain
26	chr11:48100000-48104600	Enhancers	Brain Anterior Caudate	brain
27	chr11:48100000-48106200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:48100400-48104400	Enhancers	Primary B cells from peripheral blood	blood
29	chr11:48100400-48104600	Enhancers	Brain Cingulate Gyrus	brain
30	chr11:48100400-48105400	Enhancers	Placenta	Placenta
31	chr11:48100600-48102600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:48100600-48102600	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr11:48100600-48102800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr11:48100600-48105800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr11:48100800-48102800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:48100800-48102800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:48100800-48103800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr11:48100800-48104800	Enhancers	Spleen	Spleen
39	chr11:48101000-48104600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:48101000-48104800	Enhancers	Adipose Nuclei	Adipose
41	chr11:48101200-48102400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:48101200-48104800	Enhancers	Primary T cells fromperipheralblood	blood
43	chr11:48101200-48105800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr11:48101200-48108000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr11:48101400-48102600	Weak transcription	Fetal Stomach	stomach
46	chr11:48101400-48103600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr11:48101400-48104600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr11:48101600-48102600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:48101600-48106000	Enhancers	Liver	Liver
50	chr11:48101800-48102800	Enhancers	NH-A	brain

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