Variant report

Variant	rs7043516
Chromosome Location	chr9:100617433-100617434
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100617184..100619335-chr9:100637041..100639858,3	MCF-7	breast:
2	chr9:100616472..100617973-chr9:100620292..100623040,2	K562	blood:
3	chr9:100614821..100616567-chr9:100616970..100619601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178919	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10046805	0.83[AFR][1000 genomes]
rs10119795	0.82[YRI][hapmap]
rs10512256	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs1059003	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs10983892	0.81[AMR][1000 genomes]
rs10983893	0.81[AMR][1000 genomes]
rs10983896	0.81[AMR][1000 genomes]
rs10983920	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10984009	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs10984098	0.93[CEU][hapmap]
rs10984377	0.93[CEU][hapmap]
rs10984516	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs10984522	0.83[CEU][hapmap]
rs10984532	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs12347191	0.84[AFR][1000 genomes]
rs12348304	0.82[AFR][1000 genomes]
rs12375612	0.93[CEU][hapmap]
rs1348387	0.93[CEU][hapmap]
rs1443434	0.85[ASW][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs1443435	0.86[ASW][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs17687621	0.93[CEU][hapmap]
rs1822416	0.81[ASN][1000 genomes]
rs1867277	0.81[AFR][1000 genomes]
rs1867278	0.86[ASW][hapmap];0.91[YRI][hapmap]
rs1867280	0.82[AFR][1000 genomes]
rs1947015	0.82[CEU][hapmap]
rs2401638	0.81[ASN][1000 genomes]
rs3758248	0.83[AFR][1000 genomes]
rs3758249	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs3758251	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs41274260	0.89[ASN][1000 genomes]
rs4460498	0.80[AFR][1000 genomes]
rs4742708	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs4743137	0.90[EUR][1000 genomes]
rs4743144	0.88[CEU][hapmap]
rs4743149	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs72753507	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753508	0.83[AMR][1000 genomes]
rs72753509	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851498	0.80[CEU][hapmap]
rs7851552	0.82[AFR][1000 genomes]
rs7854948	0.93[CEU][hapmap]
rs7859751	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs894673	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs907577	0.86[ASW][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv825000	chr9:100613121-100618319	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3330300	chr9:100613506-100618154	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3421459	chr9:100614656-100617704	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7043516	C9orf156	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100613400-100618800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:100613600-100618000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr9:100613800-100617800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr9:100614000-100617800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr9:100614000-100617800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:100616600-100617600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:100616600-100617600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr9:100616600-100617600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr9:100616600-100617600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
10	chr9:100616600-100617600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
11	chr9:100616800-100617600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:100616800-100617600	ZNF genes & repeats	Spleen	Spleen
13	chr9:100616800-100618000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:100616800-100618400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:100617000-100617600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr9:100617000-100617600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:100617000-100617800	Flanking Active TSS	A549	lung
18	chr9:100617000-100618200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr9:100617200-100617600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr9:100617200-100617600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
21	chr9:100617200-100617600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
22	chr9:100617200-100617600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:100617200-100617600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:100617200-100617600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:100617200-100617600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:100617200-100617800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr9:100617200-100617800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
28	chr9:100617200-100617800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
29	chr9:100617200-100618000	Bivalent/Poised TSS	Thymus	Thymus
30	chr9:100617200-100618200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr9:100617200-100618600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
32	chr9:100617400-100617600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
33	chr9:100617400-100617600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
34	chr9:100617400-100617600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
35	chr9:100617400-100617600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
36	chr9:100617400-100617600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
37	chr9:100617400-100617600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
38	chr9:100617400-100617600	Bivalent Enhancer	Fetal Intestine Small	intestine
39	chr9:100617400-100617600	Bivalent Enhancer	Fetal Thymus	thymus
40	chr9:100617400-100617600	Enhancers	Pancreas	Pancrea
41	chr9:100617400-100617600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
42	chr9:100617400-100617600	Flanking Active TSS	Hela-S3	cervix
43	chr9:100617400-100617800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
44	chr9:100617400-100617800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
45	chr9:100617400-100617800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:100617400-100617800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
47	chr9:100617400-100618000	Bivalent Enhancer	Esophagus	oesophagus

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