Variant report

Variant	rs6474916
Chromosome Location	chr9:15424291-15424292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:56083086..56085615-chr9:15422777..15425325,2	MCF-7	breast:
2	chr9:15306135..15309581-chr9:15420818..15425516,6	MCF-7	breast:
3	chr9:15420595..15424773-chr9:15424796..15433036,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136450	Chromatin interaction
ENSG00000251834	Chromatin interaction
ENSG00000155158	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10081655	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10115540	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10117968	0.94[CHB][hapmap]
rs1033056	0.83[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes]
rs10733292	0.81[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10738392	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10738393	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10738395	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs10738397	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10756664	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10756666	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10962036	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1123038	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12093	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs1397214	0.93[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs1397215	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1567452	0.83[ASN][1000 genomes]
rs1976599	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2136710	0.82[ASN][1000 genomes]
rs2175258	0.82[ASN][1000 genomes]
rs2175259	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2382530	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2665504	0.84[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap]
rs2737829	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2737842	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs2777950	0.89[YRI][hapmap]
rs4510953	0.82[AMR][1000 genomes]
rs4741500	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4741501	0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4741502	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4741504	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs4741505	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4741506	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs4741507	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes]
rs4741508	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes]
rs6474915	0.88[CHB][hapmap]
rs6474918	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6474923	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs7021042	0.86[CEU][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs7026910	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7026970	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7042165	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7046713	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs907075	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs907076	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9650682	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs9650683	0.94[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats 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	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv831520	chr9:15404866-15444447	Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15422000-15424400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:15422000-15424600	Active TSS	NHDF-Ad	bronchial
3	chr9:15422000-15424600	Active TSS	NHLF	lung
4	chr9:15422000-15424800	Active TSS	K562	blood
5	chr9:15422200-15424400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:15422200-15424400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:15422200-15424600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:15422200-15424600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:15422200-15424600	Active TSS	Fetal Brain Male	brain
10	chr9:15422200-15424800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:15422200-15424800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:15422400-15424400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:15422400-15424400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr9:15422400-15424400	Active TSS	Fetal Intestine Large	intestine
15	chr9:15422400-15424400	Active TSS	Fetal Lung	lung
16	chr9:15422400-15424400	Active TSS	NHEK	skin
17	chr9:15422400-15424600	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr9:15422400-15424600	Active TSS	A549	lung
19	chr9:15422400-15424600	Active TSS	NH-A	brain
20	chr9:15422400-15424800	Active TSS	GM12878-XiMat	blood
21	chr9:15422600-15424600	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr9:15422600-15424600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr9:15422600-15424600	Active TSS	Fetal Brain Female	brain
24	chr9:15422600-15424600	Active TSS	HMEC	breast
25	chr9:15422600-15424800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:15422800-15424400	Active TSS	Stomach Smooth Muscle	stomach
27	chr9:15423400-15424400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr9:15423400-15425200	Weak transcription	Spleen	Spleen
29	chr9:15423600-15424800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:15423600-15425200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:15423600-15434400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:15423600-15439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:15423800-15424400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
34	chr9:15423800-15424400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:15423800-15424400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr9:15423800-15424400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr9:15423800-15424600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:15423800-15424800	Weak transcription	Placenta	Placenta
39	chr9:15424000-15424400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr9:15424000-15424400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:15424000-15424400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr9:15424000-15424400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:15424000-15424400	Transcr. at gene 5' and 3'	Dnd41	blood
44	chr9:15424000-15424400	Flanking Active TSS	Osteobl	bone
45	chr9:15424000-15424600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:15424000-15424600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr9:15424000-15424600	Flanking Active TSS	HUVEC	blood vessel
48	chr9:15424000-15424800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:15424000-15424800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr9:15424000-15424800	Enhancers	Primary hematopoietic stem cells	blood

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