Variant report

Variant	rs2290505
Chromosome Location	chr17:18137141-18137142
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	POLR2A	chr17:18136952-18137389	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18135795..18137603-chr17:18160135..18163013,2	MCF-7	breast:
2	chr17:18128887..18137475-chr17:18144772..18151698,11	K562	blood:
3	chr17:18136077..18142771-chr17:18143654..18157956,22	MCF-7	breast:
4	chr17:18135872..18138183-chr17:18147458..18150169,3	K562	blood:

Variant related genes	Relation type
LLGL1	TF binding region
ENSG00000177731	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11867895	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11868708	0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11869582	0.88[EUR][1000 genomes]
rs11869952	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11872031	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12449313	0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12451555	0.85[EUR][1000 genomes]
rs12451698	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12939851	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16961114	0.92[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16961133	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16961153	0.94[JPT][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1925	0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1962949	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1962950	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2071242	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273029	0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2290502	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290503	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290504	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294913	0.94[JPT][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28364628	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35738574	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3817992	0.83[JPT][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3829956	0.94[JPT][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3862147	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889544	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4386179	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4450455	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4500798	0.92[JPT][hapmap]
rs4556848	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925151	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925177	0.94[JPT][hapmap]
rs57490980	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57697650	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59366579	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62072507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62072509	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62072511	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62072515	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62072537	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62072540	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62072541	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6502641	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7211573	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215678	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405677	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7498	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8081042	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8081155	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8081343	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9909104	0.94[JPT][hapmap]
rs9910090	0.93[JPT][hapmap]
rs9913139	0.81[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9913266	0.88[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv543246	chr17:18121007-18165604	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
11	nsv9503	chr17:18121474-18169166	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers 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	21 gene(s)	inside rSNPs	diseases
12	nsv907776	chr17:18122485-18170948	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv907777	chr17:18131087-18163262	Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18129600-18148400	Weak transcription	Small Intestine	intestine
2	chr17:18130000-18137200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:18130000-18145400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr17:18130000-18148200	Weak transcription	Fetal Kidney	kidney
5	chr17:18130000-18148200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:18130000-18149200	Weak transcription	Psoas Muscle	Psoas
7	chr17:18130200-18137400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr17:18130200-18137400	Weak transcription	Colonic Mucosa	Colon
9	chr17:18130200-18138000	Weak transcription	HUVEC	blood vessel
10	chr17:18130200-18139600	Weak transcription	Primary B cells from cord blood	blood
11	chr17:18130200-18145600	Weak transcription	A549	lung
12	chr17:18130200-18147000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr17:18130200-18147000	Weak transcription	Liver	Liver
14	chr17:18130200-18150800	Weak transcription	Right Atrium	heart
15	chr17:18130400-18137400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:18130400-18138000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr17:18130400-18138400	Weak transcription	HSMMtube	muscle
18	chr17:18130400-18138600	Weak transcription	HSMM	muscle
19	chr17:18130400-18139200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr17:18130400-18142400	Weak transcription	Fetal Heart	heart
21	chr17:18130400-18146200	Weak transcription	NHDF-Ad	bronchial
22	chr17:18130400-18148200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr17:18130600-18138600	Weak transcription	NH-A	brain
24	chr17:18130600-18148200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr17:18130800-18138000	Weak transcription	Colon Smooth Muscle	Colon
26	chr17:18131200-18148400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr17:18133200-18137600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:18133600-18137200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:18133600-18137200	Weak transcription	HepG2	liver
30	chr17:18134600-18149600	Strong transcription	Fetal Intestine Small	intestine
31	chr17:18134600-18150800	Weak transcription	Fetal Brain Male	brain
32	chr17:18134600-18150800	Strong transcription	Fetal Stomach	stomach
33	chr17:18134800-18138800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr17:18134800-18142000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr17:18135000-18149400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr17:18135200-18138200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr17:18135200-18138400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:18135200-18138400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr17:18135200-18141600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:18135200-18149400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr17:18135200-18149400	Strong transcription	Fetal Intestine Large	intestine
42	chr17:18135200-18149600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:18135200-18150000	Strong transcription	Fetal Muscle Leg	muscle
44	chr17:18135200-18150600	Strong transcription	Brain Germinal Matrix	brain
45	chr17:18135200-18160000	Strong transcription	Fetal Brain Female	brain
46	chr17:18135400-18137400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr17:18135400-18137400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr17:18135400-18138200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr17:18135400-18138400	Strong transcription	Spleen	Spleen
50	chr17:18135400-18138800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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