Variant report

Variant	rs1713493
Chromosome Location	chr17:45194762-45194763
allele	C/T
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	POLR2A	chr17:45194370-45194839	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:45190767-45195015	K562	blood:	n/a	n/a
3	POLR2A	chr17:45194624-45194808	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000221016	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1102461	0.86[YRI][hapmap]
rs1106950	0.95[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs11653589	0.83[JPT][hapmap]
rs1476498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1634265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1634269	0.80[YRI][hapmap]
rs221596	0.86[YRI][hapmap]
rs221605	0.86[YRI][hapmap]
rs221607	0.86[YRI][hapmap]
rs2678693	0.86[YRI][hapmap]
rs3851792	0.83[JPT][hapmap]
rs8068715	0.83[JPT][hapmap]
rs8071243	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs858670	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs858677	0.88[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];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs858678	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs867859	0.95[CEU][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats 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	9 gene(s)	inside rSNPs	diseases
7	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv521632	chr17:45151549-45196190	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv908563	chr17:45158537-45230311	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv962456	chr17:45163689-45212872	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1713493	HSPB9	cis	cerebellum	SCAN
rs1713493	TUBG1	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45183400-45197400	Weak transcription	HSMMtube	muscle
2	chr17:45185600-45206400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:45186800-45197800	Weak transcription	Fetal Brain Female	brain
4	chr17:45188200-45197800	Weak transcription	Hela-S3	cervix
5	chr17:45189000-45196600	Weak transcription	NHDF-Ad	bronchial
6	chr17:45189800-45198000	Weak transcription	Fetal Stomach	stomach
7	chr17:45190000-45203200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr17:45191000-45197200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr17:45191000-45202000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr17:45191200-45197800	Weak transcription	Small Intestine	intestine
11	chr17:45191200-45202600	Weak transcription	Right Ventricle	heart
12	chr17:45191400-45197200	Weak transcription	Fetal Heart	heart
13	chr17:45191400-45197200	Weak transcription	Fetal Intestine Large	intestine
14	chr17:45191600-45195600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:45191600-45196800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr17:45191600-45197600	Weak transcription	HepG2	liver
17	chr17:45191800-45197600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr17:45191800-45198000	Weak transcription	Thymus	Thymus
19	chr17:45192000-45198200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:45192200-45198000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:45192200-45198000	Weak transcription	Left Ventricle	heart
22	chr17:45192400-45195400	Weak transcription	Liver	Liver
23	chr17:45192400-45196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:45192400-45196000	Weak transcription	K562	blood
25	chr17:45192400-45196600	Weak transcription	Placenta	Placenta
26	chr17:45192400-45197000	Weak transcription	Primary B cells from cord blood	blood
27	chr17:45192400-45197400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr17:45192400-45197600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr17:45192400-45212800	Weak transcription	Gastric	stomach
30	chr17:45192600-45196000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:45192600-45197200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr17:45192600-45197200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr17:45192600-45197400	Weak transcription	Psoas Muscle	Psoas
34	chr17:45192600-45197600	Weak transcription	Fetal Kidney	kidney
35	chr17:45192600-45200200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr17:45192800-45195400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr17:45192800-45195400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr17:45192800-45197400	Weak transcription	HMEC	breast
39	chr17:45192800-45197600	Weak transcription	Primary T cells from cord blood	blood
40	chr17:45193000-45196000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr17:45193000-45197200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr17:45193200-45195400	Weak transcription	Fetal Thymus	thymus
43	chr17:45193200-45195600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:45193200-45197800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr17:45193200-45212800	Weak transcription	Aorta	Aorta
46	chr17:45193400-45197200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr17:45193400-45197400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr17:45193400-45197600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr17:45193600-45197400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr17:45193800-45195600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links