Variant report

Variant	rs9405152
Chromosome Location	chr6:1868239-1868240
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	chr6:1868113..1870293-chr6:1878428..1880757,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1467594	0.88[EUR][1000 genomes]
rs1543538	0.85[EUR][1000 genomes]
rs2281760	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2296131	0.83[EUR][1000 genomes]
rs3778537	0.84[EUR][1000 genomes]
rs3778538	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778540	0.87[EUR][1000 genomes]
rs3800091	0.84[EUR][1000 genomes]
rs3800097	0.87[EUR][1000 genomes]
rs3800099	0.87[EUR][1000 genomes]
rs3800100	0.87[EUR][1000 genomes]
rs3800103	0.87[EUR][1000 genomes]
rs3800104	0.87[EUR][1000 genomes]
rs3800107	0.88[EUR][1000 genomes]
rs3823277	0.87[EUR][1000 genomes]
rs6940806	0.85[EUR][1000 genomes]
rs912310	0.90[ASN][1000 genomes]
rs9378661	0.85[AMR][1000 genomes]
rs9391935	0.84[EUR][1000 genomes]
rs9392341	0.85[AMR][1000 genomes]
rs9405522	0.84[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	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1019895	chr6:1832936-1882435	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1842800-1872400	Weak transcription	Gastric	stomach
2	chr6:1851200-1895600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:1851400-1872200	Weak transcription	Pancreas	Pancrea
4	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:1856800-1869600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:1857600-1877200	Weak transcription	Primary T cells from cord blood	blood
7	chr6:1861400-1870400	Weak transcription	Colonic Mucosa	Colon
8	chr6:1861600-1870000	Weak transcription	Aorta	Aorta
9	chr6:1865200-1869600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:1865200-1884600	Weak transcription	Small Intestine	intestine
11	chr6:1865400-1869400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:1865400-1869600	Weak transcription	Ovary	ovary
13	chr6:1865400-1870600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:1865400-1871000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:1865600-1869200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:1865800-1870200	Weak transcription	Brain Anterior Caudate	brain
17	chr6:1865800-1872200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:1866000-1869600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:1866400-1869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:1866400-1870000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:1866400-1870600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:1866400-1871600	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:1866600-1870600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:1866600-1872000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:1866800-1869400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:1866800-1869400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:1866800-1871200	Weak transcription	Fetal Kidney	kidney
28	chr6:1867000-1869200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:1867000-1869200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:1867000-1872000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:1867000-1873800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:1867200-1869200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:1867200-1869400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:1867200-1869400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:1867200-1869400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:1867200-1871800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:1867200-1872200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:1867400-1870000	Weak transcription	HepG2	liver
39	chr6:1868000-1868800	Enhancers	GM12878-XiMat	blood
40	chr6:1868000-1873600	Weak transcription	Stomach Mucosa	stomach

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