Variant report

Variant	rs17018997
Chromosome Location	chr1:212585092-212585093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212457988..212460167-chr1:212585002..212587734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10494951	0.81[TSI][hapmap]
rs11590242	0.81[TSI][hapmap]
rs11803766	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239580	0.81[MKK][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes]
rs12739715	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12755383	1.00[EUR][1000 genomes]
rs2120770	0.84[TSI][hapmap]
rs2166155	0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs35702733	0.99[EUR][1000 genomes]
rs35822123	0.83[EUR][1000 genomes]
rs4336916	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4540733	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6666415	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6669027	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6676208	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs6693849	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6697910	1.00[CEU][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704234	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71646158	0.83[EUR][1000 genomes]
rs71646159	0.94[EUR][1000 genomes]
rs71646161	1.00[EUR][1000 genomes]
rs7518399	0.83[TSI][hapmap]
rs7533689	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7551910	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17018997	LOC148696	cis	parietal	SCAN
rs17018997	C1orf74	cis	parietal	SCAN
rs17018997	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs17018997	BATF3	cis	cerebellum	SCAN
rs17018997	RP11-15I11.3	cis	lung	GTEx
rs17018997	RP11-15I11.3	cis	Thyroid	GTEx
rs17018997	ATF3	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
2	chr1:212571000-212586200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:212572800-212585600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:212575200-212585800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:212575600-212585200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:212576000-212585200	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr1:212576200-212585200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:212576200-212585200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:212577200-212586200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:212577200-212586200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:212577800-212586600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:212578000-212585800	Strong transcription	Primary T cells from cord blood	blood
13	chr1:212578000-212586000	Strong transcription	Fetal Thymus	thymus
14	chr1:212578600-212585200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:212578600-212585200	Strong transcription	Fetal Brain Female	brain
16	chr1:212579800-212587000	Weak transcription	Right Atrium	heart
17	chr1:212580000-212585600	Strong transcription	Brain Hippocampus Middle	brain
18	chr1:212580600-212587200	Weak transcription	HSMMtube	muscle
19	chr1:212580800-212585200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:212580800-212585200	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:212580800-212585400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:212580800-212586200	Strong transcription	Fetal Stomach	stomach
23	chr1:212580800-212586600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:212580800-212587000	Weak transcription	NHDF-Ad	bronchial
25	chr1:212581200-212585600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:212581200-212585600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:212583200-212586800	Weak transcription	HMEC	breast
28	chr1:212583200-212587000	Weak transcription	Fetal Heart	heart
29	chr1:212583200-212587000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:212583400-212586800	Weak transcription	HUVEC	blood vessel
31	chr1:212583600-212586800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:212583600-212587000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr1:212583600-212587000	Weak transcription	Hela-S3	cervix
34	chr1:212583800-212585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:212583800-212586600	Weak transcription	Colonic Mucosa	Colon
36	chr1:212583800-212586600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:212583800-212587000	Weak transcription	Right Ventricle	heart
38	chr1:212583800-212587000	Weak transcription	A549	lung
39	chr1:212583800-212587000	Weak transcription	NH-A	brain
40	chr1:212584000-212587000	Weak transcription	Fetal Kidney	kidney
41	chr1:212584000-212587200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:212584000-212587400	Weak transcription	Ovary	ovary
43	chr1:212584200-212585400	Genic enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:212584200-212586400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:212584200-212586600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:212584200-212586800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:212584200-212586800	Weak transcription	Adipose Nuclei	Adipose
48	chr1:212584200-212586800	Weak transcription	Esophagus	oesophagus
49	chr1:212584200-212586800	Weak transcription	Placenta	Placenta
50	chr1:212584200-212587000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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