Variant report

Variant	rs6559756
Chromosome Location	chr9:86621533-86621534
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86621080..86624737-chr9:86626977..86631058,3	MCF-7	breast:
2	chr9:86594505..86596949-chr9:86620921..86622582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165119	Chromatin interaction
ENSG00000178966	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10124390	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs10780639	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10780640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10868071	0.82[YRI][hapmap]
rs10868077	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868079	0.83[CHB][hapmap]
rs10868080	0.82[AFR][1000 genomes]
rs11140340	0.94[JPT][hapmap]
rs12004439	0.81[AMR][1000 genomes]
rs12006540	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12551039	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13296528	0.82[YRI][hapmap]
rs1572030	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs1572031	0.83[CHB][hapmap]
rs177042	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1831757	0.80[YRI][hapmap]
rs1982151	0.84[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2065516	0.83[CHB][hapmap]
rs2780103	0.82[YRI][hapmap]
rs2780142	0.83[CHB][hapmap]
rs295274	0.83[CHB][hapmap]
rs296885	0.83[CHB][hapmap]
rs296887	0.89[YRI][hapmap]
rs296888	0.86[YRI][hapmap]
rs296889	0.84[LWK][hapmap];0.89[YRI][hapmap]
rs296890	0.89[YRI][hapmap]
rs296891	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs296892	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs296893	0.86[YRI][hapmap]
rs4147132	0.82[YRI][hapmap]
rs4535826	0.82[YRI][hapmap]
rs4877814	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];0.99[ASN][1000 genomes]
rs4877815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5018100	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6559750	0.83[CHB][hapmap]
rs6559753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6559754	0.95[CHB][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7020841	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7021189	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7045008	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs754144	0.83[CHB][hapmap]
rs7864367	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7869321	0.82[YRI][hapmap]
rs7869387	0.83[CHB][hapmap]
rs7875011	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7875242	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7875289	0.82[CHB][hapmap]
rs796000	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs796001	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs796002	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][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	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv3328820	chr9:86613612-86634313	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6559756	RMI1	cis	parietal	SCAN
rs6559756	C9orf64	cis	parietal	SCAN
rs6559756	C9orf64	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
2	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:86597000-86621600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:86597400-86628800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:86598800-86622400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:86602000-86623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:86602400-86627200	Weak transcription	Left Ventricle	heart
8	chr9:86604000-86622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:86604000-86626200	Weak transcription	Pancreas	Pancrea
10	chr9:86604200-86623400	Weak transcription	Fetal Stomach	stomach
11	chr9:86605000-86622400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:86605400-86622200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:86606000-86624200	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:86607800-86622600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:86607800-86622800	Weak transcription	K562	blood
16	chr9:86611000-86623000	Weak transcription	Psoas Muscle	Psoas
17	chr9:86616800-86621600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:86616800-86621800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:86616800-86623800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:86617000-86621600	Weak transcription	Fetal Lung	lung
21	chr9:86617000-86621600	Weak transcription	Fetal Thymus	thymus
22	chr9:86617000-86622200	Weak transcription	Fetal Brain Female	brain
23	chr9:86617000-86622600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:86617000-86622800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:86617000-86622800	Weak transcription	Fetal Kidney	kidney
26	chr9:86617400-86621600	Weak transcription	Primary B cells from cord blood	blood
27	chr9:86617600-86621600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:86617600-86621600	Weak transcription	HUVEC	blood vessel
29	chr9:86617600-86624400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:86617600-86624800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr9:86617600-86625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:86617800-86623600	Weak transcription	A549	lung
33	chr9:86617800-86625800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr9:86618200-86625400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr9:86618400-86621600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:86618400-86625400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:86618800-86624400	Weak transcription	Aorta	Aorta
38	chr9:86619800-86624400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:86620200-86621800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:86620200-86622200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:86620200-86622400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:86620200-86622800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:86620200-86623400	Weak transcription	Dnd41	blood
44	chr9:86621200-86621600	Enhancers	Stomach Mucosa	stomach
45	chr9:86621400-86622000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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