Variant report

Variant	rs4741498
Chromosome Location	chr9:15424938-15424939
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
ENSG00000164975	Chromatin interaction
ENSG00000155158	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10081655	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10115540	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10122299	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10738392	0.84[EUR][1000 genomes]
rs10738395	0.81[CEU][hapmap]
rs10756663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10756664	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10756665	0.86[EUR][1000 genomes]
rs10756667	0.81[EUR][1000 genomes]
rs10756669	0.81[EUR][1000 genomes]
rs1123038	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1397215	1.00[CEU][hapmap]
rs1976599	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1983207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2136709	0.83[AMR][1000 genomes]
rs2136710	0.86[EUR][1000 genomes]
rs2175258	0.86[EUR][1000 genomes]
rs2382529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2487860	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2737828	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2737829	1.00[CEU][hapmap]
rs2737835	1.00[CEU][hapmap]
rs2737842	1.00[CEU][hapmap]
rs4741500	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4741503	0.81[EUR][1000 genomes]
rs4741504	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4741506	1.00[CEU][hapmap]
rs55791531	0.80[ASN][1000 genomes]
rs55993183	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6474918	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6474923	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7023290	0.83[EUR][1000 genomes]
rs7026970	1.00[CEU][hapmap];1.00[MKK][hapmap];0.83[EUR][1000 genomes]
rs7034447	0.81[EUR][1000 genomes]
rs7040353	0.86[EUR][1000 genomes]
rs7042165	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7046713	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7470323	0.81[EUR][1000 genomes]
rs9650683	1.00[CEU][hapmap];0.81[EUR][1000 genomes]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4741498	HSS00006524	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15423400-15425200	Weak transcription	Spleen	Spleen
2	chr9:15423600-15425200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:15423600-15434400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:15423600-15439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:15424000-15425000	Weak transcription	Lung	lung
6	chr9:15424000-15425200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr9:15424000-15425200	Weak transcription	Esophagus	oesophagus
8	chr9:15424000-15425200	Weak transcription	Gastric	stomach
9	chr9:15424000-15425200	Weak transcription	Pancreas	Pancrea
10	chr9:15424000-15425400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr9:15424000-15425600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:15424000-15427600	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr9:15424000-15430200	Weak transcription	Small Intestine	intestine
14	chr9:15424000-15431000	Weak transcription	Psoas Muscle	Psoas
15	chr9:15424000-15443400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:15424000-15443600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:15424200-15425000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr9:15424200-15425000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr9:15424200-15425000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:15424200-15425000	Enhancers	Brain Germinal Matrix	brain
21	chr9:15424200-15425000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr9:15424200-15425000	Weak transcription	Right Ventricle	heart
23	chr9:15424200-15425000	Weak transcription	HSMMtube	muscle
24	chr9:15424200-15425200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:15424200-15425200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr9:15424200-15425200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:15424200-15425200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr9:15424200-15425200	Weak transcription	Thymus	Thymus
29	chr9:15424200-15425400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:15424200-15425400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:15424200-15425400	Enhancers	Brain Angular Gyrus	brain
32	chr9:15424200-15425600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:15424200-15425600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:15424200-15425600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr9:15424200-15425600	Weak transcription	Aorta	Aorta
36	chr9:15424200-15425800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr9:15424200-15425800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr9:15424200-15426000	Weak transcription	Right Atrium	heart
39	chr9:15424200-15426600	Enhancers	Fetal Heart	heart
40	chr9:15424200-15426600	Strong transcription	Fetal Muscle Leg	muscle
41	chr9:15424200-15426800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:15424400-15425000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:15424400-15425000	Weak transcription	Fetal Intestine Large	intestine
44	chr9:15424400-15425000	Genic enhancers	Rectal Mucosa Donor 29	rectum
45	chr9:15424400-15425000	Genic enhancers	Osteobl	bone
46	chr9:15424400-15426600	Genic enhancers	Dnd41	blood
47	chr9:15424600-15425000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:15424600-15425000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
49	chr9:15424600-15425000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
50	chr9:15424600-15425000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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