Variant report

Variant	rs6479434
Chromosome Location	chr9:95630981-95630982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95630451..95632517-chr9:95636890..95640769,3	MCF-7	breast:
2	chr9:95630810..95632810-chr9:95646965..95649484,2	MCF-7	breast:
3	chr9:95624512..95626561-chr9:95630014..95632594,2	K562	blood:
4	chr9:95630407..95632096-chr9:95638470..95640204,2	K562	blood:

Variant related genes	Relation type
ENSG00000127081	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10115872	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123870	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10156497	0.95[ASN][1000 genomes]
rs1022833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739932	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761172	0.95[ASN][1000 genomes]
rs10761175	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10821021	0.95[ASN][1000 genomes]
rs10821022	0.95[ASN][1000 genomes]
rs10821027	0.82[EUR][1000 genomes]
rs10821028	0.95[ASN][1000 genomes]
rs10821030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821031	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821032	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821035	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821040	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992489	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992529	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12003440	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs12336022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337654	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12338961	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12346689	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12379300	0.95[ASN][1000 genomes]
rs13288901	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13293147	0.86[JPT][hapmap]
rs13294147	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2296060	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28700150	0.92[ASN][1000 genomes]
rs36194652	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3824428	0.95[ASN][1000 genomes]
rs4078292	0.86[JPT][hapmap]
rs4133033	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4510923	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4535796	0.87[ASN][1000 genomes]
rs4538949	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4626670	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4744150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744151	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7032277	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035868	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7035881	0.86[JPT][hapmap]
rs7039812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7043469	0.86[JPT][hapmap]
rs7045305	0.95[ASN][1000 genomes]
rs7047181	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7847713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847998	0.95[ASN][1000 genomes]
rs7859380	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7869480	0.95[ASN][1000 genomes]
rs7872848	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7872987	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7873021	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873954	0.81[EUR][1000 genomes]
rs7874026	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775485	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv893574	chr9:95580376-95688099	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6479434	C9orf102	cis	parietal	SCAN
rs6479434	SUSD3	cis	multi-tissue	Pritchard
rs6479434	ZNF484	cis	parietal	SCAN
rs6479434	ZNF484	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95609000-95639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:95611200-95632800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:95616200-95639800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:95616400-95632800	Weak transcription	Gastric	stomach
5	chr9:95616400-95639800	Weak transcription	Small Intestine	intestine
6	chr9:95616600-95639600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:95618200-95639800	Weak transcription	Colonic Mucosa	Colon
8	chr9:95618400-95637600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:95618400-95638600	Weak transcription	K562	blood
10	chr9:95618600-95638000	Weak transcription	Brain Anterior Caudate	brain
11	chr9:95619600-95638600	Weak transcription	Brain Angular Gyrus	brain
12	chr9:95622400-95631600	Weak transcription	Osteobl	bone
13	chr9:95622400-95632800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:95622400-95632800	Weak transcription	Thymus	Thymus
15	chr9:95622400-95635200	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:95622400-95637600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:95622400-95637800	Weak transcription	Hela-S3	cervix
18	chr9:95622400-95638000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:95622400-95638000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:95622400-95638600	Weak transcription	HMEC	breast
21	chr9:95622400-95638600	Weak transcription	NHDF-Ad	bronchial
22	chr9:95622400-95638800	Weak transcription	NHLF	lung
23	chr9:95622600-95631600	Weak transcription	Fetal Lung	lung
24	chr9:95622600-95632600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:95622600-95632800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:95622600-95632800	Weak transcription	Fetal Brain Female	brain
27	chr9:95622600-95633800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:95622600-95635000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:95622600-95637600	Weak transcription	Esophagus	oesophagus
30	chr9:95622600-95637600	Weak transcription	Spleen	Spleen
31	chr9:95622600-95638800	Weak transcription	Brain Substantia Nigra	brain
32	chr9:95622600-95639000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:95622600-95639000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:95622600-95639000	Weak transcription	NH-A	brain
35	chr9:95622600-95639400	Weak transcription	HSMMtube	muscle
36	chr9:95622600-95639600	Weak transcription	Fetal Kidney	kidney
37	chr9:95622600-95639800	Weak transcription	Aorta	Aorta
38	chr9:95623200-95632400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:95623200-95632600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:95623200-95632800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:95623200-95637600	Weak transcription	Ovary	ovary
42	chr9:95623200-95639000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:95623200-95639400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr9:95623600-95639200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:95623800-95637200	Weak transcription	Fetal Brain Male	brain
46	chr9:95624200-95632600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr9:95625600-95632800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr9:95625600-95639600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:95626000-95633200	Strong transcription	Primary T cells from cord blood	blood
50	chr9:95626000-95634200	Strong transcription	Primary B cells from cord blood	blood

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