Variant report

Variant	rs17624006
Chromosome Location	chr6:36930687-36930688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:36930512-36931164	GM12878	blood:	n/a	n/a
2	RCOR1	chr6:36930658-36930986	K562	blood:	n/a	n/a
3	SIN3A	chr6:36930622-36931114	H1-hESC	embryonic stem cell:	n/a	n/a
4	ELF1	chr6:36930543-36931897	GM12878	blood:	n/a	n/a
5	SRF	chr6:36930636-36930890	GM12878	blood:	n/a	n/a
6	GABPA	chr6:36930633-36931027	K562	blood:	n/a	n/a
7	ELF1	chr6:36930592-36931136	GM12878	blood:	n/a	n/a
8	CEBPB	chr6:36930679-36931239	ECC-1	luminal epithelium:	n/a	n/a
9	SPI1	chr6:36930669-36931139	HL-60	blood:	n/a	n/a
10	SPI1	chr6:36930666-36931141	GM12891	blood:	n/a	n/a
11	SPI1	chr6:36930546-36931202	HL-60	blood:	n/a	n/a
12	MTA3	chr6:36930555-36931572	GM12878	blood:	n/a	n/a
13	ELF1	chr6:36930647-36931098	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36929829..36933522-chr6:36953197..36956380,5	MCF-7	breast:

Variant related genes	Relation type
PI16	TF binding region
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs41272194	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272198	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58012316	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406491	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406492	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406493	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406498	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406499	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406518	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406522	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6938178	1.00[CHD][hapmap]
rs708005	0.93[EUR][1000 genomes]
rs708006	0.85[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs72846863	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72846873	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72848004	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740320	1.00[CHB][hapmap]
rs9380622	1.00[ASW][hapmap]
rs9470445	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17624006	PI16	cis	Brain Pons	GTEx
rs17624006	SRSF3	cis	parietal	SCAN
rs17624006	PI16	cis	cerebellum	SCAN
rs17624006	PI16	cis	parietal	SCAN
rs17624006	ZFAND3	cis	parietal	SCAN
rs17624006	CDKN1A	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36917600-36931200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:36921800-36931200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr6:36922000-36931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:36923400-36931000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:36923400-36931000	Weak transcription	Brain Substantia Nigra	brain
6	chr6:36927000-36931600	Weak transcription	Lung	lung
7	chr6:36927200-36931000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:36927200-36931600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:36927200-36933400	Enhancers	Stomach Mucosa	stomach
10	chr6:36927400-36931000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:36927800-36933200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:36928000-36931200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:36928000-36933600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr6:36928200-36935200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:36928600-36935000	Weak transcription	HSMMtube	muscle
16	chr6:36928600-36935400	Weak transcription	Small Intestine	intestine
17	chr6:36928800-36934000	Weak transcription	HSMM	muscle
18	chr6:36928800-36935000	Weak transcription	HUVEC	blood vessel
19	chr6:36929000-36931000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:36929000-36934200	Weak transcription	Osteobl	bone
21	chr6:36929000-36934400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:36929000-36934800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:36929000-36935200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:36929000-36935400	Weak transcription	Ovary	ovary
25	chr6:36929000-36935400	Weak transcription	A549	lung
26	chr6:36929200-36931000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:36929200-36931000	Weak transcription	NHEK	skin
28	chr6:36929200-36931400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:36929200-36931400	Enhancers	Spleen	Spleen
30	chr6:36929200-36931800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:36929200-36934600	Weak transcription	NH-A	brain
32	chr6:36929400-36931000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:36929400-36931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:36929400-36931000	Weak transcription	Brain Anterior Caudate	brain
35	chr6:36929400-36931000	Weak transcription	Esophagus	oesophagus
36	chr6:36929400-36931200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:36929400-36931200	Weak transcription	Left Ventricle	heart
38	chr6:36929400-36934400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:36929400-36935200	Weak transcription	K562	blood
40	chr6:36929600-36931200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:36929600-36931200	Weak transcription	Right Atrium	heart
42	chr6:36929600-36932000	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:36929600-36932200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr6:36929600-36936800	Weak transcription	Hela-S3	cervix
45	chr6:36929800-36931200	Weak transcription	Gastric	stomach
46	chr6:36929800-36931200	Weak transcription	Pancreas	Pancrea
47	chr6:36929800-36933200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:36930000-36931000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:36930000-36931000	Weak transcription	Right Ventricle	heart
50	chr6:36930000-36933000	Enhancers	Primary B cells from cord blood	blood

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