Variant report

Variant	rs197919
Chromosome Location	chr17:45003675-45003676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45003546-45004088	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr17:45003396-45003973	K562	blood:	n/a	n/a
3	POLR2A	chr17:45002684-45003696	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45003530..45006692-chr17:45016648..45018948,3	K562	blood:
2	chr17:44976106..44978964-chr17:45002634..45004871,2	MCF-7	breast:
3	chr17:44862309..44864550-chr17:45002242..45004726,2	MCF-7	breast:
4	chr17:44974470..44976026-chr17:45001185..45003894,2	K562	blood:
5	chr17:45001648..45005787-chr17:45021612..45024553,3	K562	blood:
6	chr17:44917356..44918893-chr17:45002480..45005185,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261886	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1047779	1.00[ASN][1000 genomes]
rs1052504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052586	0.99[ASN][1000 genomes]
rs10853085	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853086	0.89[EUR][1000 genomes]
rs10853087	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079744	0.85[EUR][1000 genomes]
rs11079745	0.98[ASN][1000 genomes]
rs11652318	0.99[ASN][1000 genomes]
rs11654971	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655668	0.87[EUR][1000 genomes]
rs11656362	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11658276	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11869840	1.00[ASN][1000 genomes]
rs12601886	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940071	1.00[ASN][1000 genomes]
rs1618989	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1623402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662576	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662594	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662596	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662597	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17608961	0.99[ASN][1000 genomes]
rs1838105	0.89[EUR][1000 genomes]
rs1867237	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197912	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs197913	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs197915	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs197917	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197918	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197922	0.89[EUR][1000 genomes]
rs197923	0.89[EUR][1000 genomes]
rs197925	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197926	0.99[ASN][1000 genomes]
rs2003538	0.96[ASN][1000 genomes]
rs2003539	1.00[ASN][1000 genomes]
rs2072317	0.84[EUR][1000 genomes]
rs2191033	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316330	0.99[ASN][1000 genomes]
rs2317997	1.00[ASN][1000 genomes]
rs28553405	0.92[ASN][1000 genomes]
rs2920396	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920397	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35707546	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3760377	0.99[ASN][1000 genomes]
rs3785888	1.00[ASN][1000 genomes]
rs3809854	0.99[ASN][1000 genomes]
rs3851784	0.99[ASN][1000 genomes]
rs3851785	0.99[ASN][1000 genomes]
rs3851786	0.94[ASN][1000 genomes]
rs3851787	0.96[ASN][1000 genomes]
rs3885731	0.84[EUR][1000 genomes]
rs3890958	0.84[EUR][1000 genomes]
rs4381655	0.99[ASN][1000 genomes]
rs4602097	0.99[ASN][1000 genomes]
rs4968248	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968250	0.98[ASN][1000 genomes]
rs4968285	0.99[ASN][1000 genomes]
rs4968286	1.00[ASN][1000 genomes]
rs4968287	0.97[ASN][1000 genomes]
rs4968288	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968290	0.88[ASN][1000 genomes]
rs62075889	1.00[ASN][1000 genomes]
rs6504622	1.00[ASN][1000 genomes]
rs7213526	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225428	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342957	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736603	0.97[ASN][1000 genomes]
rs736604	1.00[ASN][1000 genomes]
rs740617	1.00[ASN][1000 genomes]
rs8065527	0.83[EUR][1000 genomes]
rs9889741	1.00[ASN][1000 genomes]
rs9889762	0.99[ASN][1000 genomes]
rs9893713	0.87[ASN][1000 genomes]
rs9898981	1.00[ASN][1000 genomes]
rs9901977	0.87[ASN][1000 genomes]
rs9911967	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs197919	GOSR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45001200-45005000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:45001200-45005000	Weak transcription	Gastric	stomach
3	chr17:45001200-45005000	Weak transcription	Lung	lung
4	chr17:45001200-45005400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:45001200-45005400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:45001200-45011400	Weak transcription	Fetal Brain Male	brain
7	chr17:45001400-45004800	Weak transcription	Fetal Thymus	thymus
8	chr17:45001400-45005200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr17:45001400-45005200	Weak transcription	Colonic Mucosa	Colon
10	chr17:45001400-45005400	Weak transcription	Esophagus	oesophagus
11	chr17:45001400-45005400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr17:45001400-45006800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:45001400-45006800	Weak transcription	Placenta	Placenta
14	chr17:45001400-45007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:45001400-45009400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:45001600-45004200	Enhancers	Stomach Mucosa	stomach
17	chr17:45001600-45005400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr17:45001600-45005400	Weak transcription	Fetal Stomach	stomach
19	chr17:45001600-45005800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr17:45001600-45005800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr17:45001600-45006000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr17:45001600-45008200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr17:45001600-45008200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:45001600-45020800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr17:45001800-45004000	Enhancers	Small Intestine	intestine
26	chr17:45001800-45004200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr17:45001800-45004400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr17:45001800-45005200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr17:45001800-45005600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr17:45001800-45006000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr17:45001800-45007000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:45001800-45007200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr17:45001800-45008200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr17:45001800-45008200	Weak transcription	HSMMtube	muscle
35	chr17:45002000-45005200	Weak transcription	Primary B cells from cord blood	blood
36	chr17:45002000-45005200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr17:45002000-45005400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:45002000-45005400	Weak transcription	Right Ventricle	heart
39	chr17:45002000-45005400	Weak transcription	NHLF	lung
40	chr17:45002000-45005800	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr17:45002000-45006200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:45002000-45006200	Weak transcription	NH-A	brain
43	chr17:45002000-45006400	Weak transcription	NHDF-Ad	bronchial
44	chr17:45002000-45006600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr17:45002000-45006800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr17:45002000-45007000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr17:45002000-45007000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr17:45002000-45007600	Weak transcription	Brain Substantia Nigra	brain
49	chr17:45002000-45008400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr17:45002000-45008400	Weak transcription	Brain Angular Gyrus	brain

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