Variant report

Variant	rs7046435
Chromosome Location	chr9:117389591-117389592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117373091..117376676-chr9:117386380..117392988,6	MCF-7	breast:
2	chr9:117386065..117390053-chr9:117395707..117398549,3	MCF-7	breast:
3	chr9:117379874..117381903-chr9:117388019..117390804,3	K562	blood:
4	chr9:117372577..117376440-chr9:117385141..117391874,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157693	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10817647	0.85[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs10817648	0.81[AMR][1000 genomes]
rs10817650	0.81[AMR][1000 genomes]
rs10817655	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10817658	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10817662	0.85[ASN][1000 genomes]
rs10817663	0.85[ASN][1000 genomes]
rs10982340	0.85[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs10982342	0.85[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs10982360	0.85[ASN][1000 genomes]
rs11792303	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12379659	0.85[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs12555934	0.85[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs13293886	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2004734	0.81[AMR][1000 genomes]
rs2274595	0.95[JPT][hapmap]
rs2418310	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2418312	0.85[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs2418314	0.81[AMR][1000 genomes]
rs2900587	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2900588	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2900590	0.94[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34251356	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4246902	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4978602	0.85[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4979447	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4979448	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs58090448	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7027369	0.81[ASW][hapmap];0.86[CEU][hapmap];0.85[TSI][hapmap]
rs7027695	1.00[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7031094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7032258	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs7034112	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7043739	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7043865	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7047395	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7047491	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7047560	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs751780	0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs756016	0.85[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs7856554	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7866831	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active 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	157 gene(s)	inside rSNPs	diseases
2	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
6	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	157 gene(s)	inside rSNPs	diseases
8	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
19	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
20	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
21	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
22	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
23	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
24	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
25	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats 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 target site	30 gene(s)	inside rSNPs	diseases
26	nsv893766	chr9:117385992-117516418	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7046435	C9orf29	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117375000-117391200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:117375000-117405200	Weak transcription	Psoas Muscle	Psoas
3	chr9:117375000-117410400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:117375200-117389800	Weak transcription	Fetal Brain Male	brain
5	chr9:117375200-117405400	Weak transcription	Small Intestine	intestine
6	chr9:117375400-117389800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:117375600-117389600	Weak transcription	Brain Germinal Matrix	brain
8	chr9:117375600-117405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:117375800-117389800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:117375800-117409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:117375800-117415600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr9:117376200-117390000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:117376200-117390000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:117376200-117415600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:117376400-117391200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:117376400-117396800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:117376600-117396200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:117379400-117390000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:117379400-117409600	Strong transcription	Dnd41	blood
20	chr9:117379600-117390000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr9:117380600-117399000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr9:117380600-117409200	Strong transcription	Primary T cells from cord blood	blood
23	chr9:117381800-117389800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr9:117382000-117396000	Weak transcription	Colonic Mucosa	Colon
25	chr9:117382000-117415000	Weak transcription	Fetal Kidney	kidney
26	chr9:117382200-117390200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:117382200-117407600	Weak transcription	Stomach Mucosa	stomach
28	chr9:117383000-117403800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:117384000-117403800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:117384200-117390200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:117384200-117407800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:117384400-117394800	Weak transcription	Right Ventricle	heart
33	chr9:117384400-117404000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr9:117384800-117393200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:117384800-117393200	Weak transcription	NHEK	skin
36	chr9:117384800-117403200	Strong transcription	GM12878-XiMat	blood
37	chr9:117384800-117408600	Strong transcription	Fetal Stomach	stomach
38	chr9:117385000-117389800	Weak transcription	Ovary	ovary
39	chr9:117385000-117391800	Weak transcription	HMEC	breast
40	chr9:117385000-117396000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:117385000-117405600	Weak transcription	HSMMtube	muscle
42	chr9:117385000-117407800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:117385000-117415600	Weak transcription	NH-A	brain
44	chr9:117385200-117389800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr9:117385200-117391000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:117385200-117394600	Weak transcription	A549	lung
47	chr9:117385800-117397200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:117385800-117408600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr9:117386200-117396200	Weak transcription	Osteobl	bone
50	chr9:117386400-117390200	Strong transcription	Spleen	Spleen

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