Variant report

Variant	rs11628333
Chromosome Location	chr14:71205727-71205728
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	chr14:71107894..71110121-chr14:71204423..71206018,2	MCF-7	breast:
2	chr14:71196902..71199011-chr14:71204967..71206734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259115	Chromatin interaction
ENSG00000133985	Chromatin interaction
ENSG00000245466	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10129495	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs10131177	0.82[ASN][1000 genomes]
rs10131364	0.81[ASN][1000 genomes]
rs10141804	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs10143748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10873243	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs11158882	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs11621281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11624934	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12886990	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs12888427	0.86[ASN][1000 genomes]
rs12897648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17108492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs1987652	0.81[ASN][1000 genomes]
rs2158530	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs2158531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs28420983	0.88[ASN][1000 genomes]
rs36570	0.80[CHD][hapmap]
rs4902843	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs4902846	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs4902849	0.86[ASN][1000 genomes]
rs66736782	0.88[ASN][1000 genomes]
rs71425216	0.88[ASN][1000 genomes]
rs8008802	0.98[ASN][1000 genomes]
rs8019261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8019448	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8019513	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs8020663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8022333	0.82[ASN][1000 genomes]
rs8022401	0.82[ASN][1000 genomes]
rs9323548	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11628333	MAP3K9	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
2	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
4	chr14:71189800-71209400	Strong transcription	Fetal Brain Female	brain
5	chr14:71190000-71214400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:71191400-71220000	Weak transcription	Fetal Brain Male	brain
7	chr14:71191600-71220200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:71192400-71220200	Weak transcription	Fetal Kidney	kidney
9	chr14:71192600-71221800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr14:71193400-71211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr14:71193600-71210200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:71193800-71209400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:71193800-71209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:71194000-71208400	Weak transcription	Brain Substantia Nigra	brain
15	chr14:71194000-71222000	Weak transcription	HSMMtube	muscle
16	chr14:71194200-71209600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr14:71194400-71210400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr14:71194400-71213400	Weak transcription	Psoas Muscle	Psoas
19	chr14:71194400-71221600	Weak transcription	Left Ventricle	heart
20	chr14:71194600-71218600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr14:71194600-71221600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr14:71195600-71209400	Strong transcription	Placenta	Placenta
23	chr14:71195600-71209600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr14:71195600-71210000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr14:71196200-71209200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr14:71196200-71217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr14:71196400-71209400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr14:71196800-71206600	Weak transcription	Aorta	Aorta
29	chr14:71197000-71228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr14:71197600-71217000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr14:71198400-71209400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr14:71198400-71223400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr14:71198800-71210000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr14:71199000-71212400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr14:71199400-71209000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr14:71199600-71209400	Strong transcription	HMEC	breast
37	chr14:71199600-71219600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:71200000-71210200	Strong transcription	NHEK	skin
39	chr14:71200200-71208800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr14:71200200-71216400	Weak transcription	Brain Hippocampus Middle	brain
41	chr14:71200400-71215400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr14:71200600-71206400	Weak transcription	Ovary	ovary
43	chr14:71200600-71208600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr14:71200600-71224200	Weak transcription	Spleen	Spleen
45	chr14:71200800-71206400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:71200800-71213000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr14:71201000-71206400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr14:71201200-71206400	Weak transcription	Brain Germinal Matrix	brain
49	chr14:71201200-71215200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr14:71201200-71228000	Weak transcription	Colonic Mucosa	Colon

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