Variant report

Variant	rs1616299
Chromosome Location	chr1:247462701-247462702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247462027..247464114-chr1:247493562..247495364,2	K562	blood:
2	chr1:247457284..247461464-chr1:247462178..247466705,7	K562	blood:
3	chr1:247461556..247465350-chr1:247467126..247471967,7	K562	blood:

Variant related genes	Relation type
ENSG00000202079	Chromatin interaction
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10754542	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10754544	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs10924983	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10924985	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs11578583	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1192830	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1192832	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12035515	0.86[ASN][1000 genomes]
rs1204493	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341173	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771929	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1771943	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778544	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778546	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2153631	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799540	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3850824	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4320815	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925532	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925533	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4925534	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4925621	0.83[ASN][1000 genomes]
rs56037169	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56399534	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674425	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6692645	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74163745	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7418221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528202	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7540329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7552292	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs875883	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426180	1.00[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426181	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426233	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9725334	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1616299	ZNF496	cis	parietal	SCAN
rs1616299	ZNF496	cis	Esophagus Muscularis	GTEx
rs1616299	ZNF496	cis	lung	GTEx
rs1616299	ZNF496	cis	Nerve Tibial	GTEx
rs1616299	EDIL3	trans	lymphoblastoid	RTeQTL
rs1616299	ZNF496	cis	Thyroid	GTEx
rs1616299	ZNF496	cis	cerebellum	SCAN
rs1616299	MAP1LC3C	cis	parietal	SCAN
rs1616299	OR2T11	cis	parietal	SCAN
rs1616299	EFCAB2	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
3	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr1:247455800-247464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
6	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
7	chr1:247457000-247465000	Weak transcription	Hela-S3	cervix
8	chr1:247457800-247463200	Weak transcription	Placenta	Placenta
9	chr1:247457800-247466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:247458000-247466800	Weak transcription	HSMMtube	muscle
11	chr1:247458200-247463000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:247459000-247463600	Weak transcription	NH-A	brain
13	chr1:247459000-247463600	Weak transcription	NHLF	lung
14	chr1:247459200-247463600	Weak transcription	Osteobl	bone
15	chr1:247459400-247463200	Weak transcription	Left Ventricle	heart
16	chr1:247459600-247463600	Weak transcription	Fetal Lung	lung
17	chr1:247459800-247485800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:247460400-247463000	Weak transcription	GM12878-XiMat	blood
19	chr1:247460400-247464000	Strong transcription	Fetal Stomach	stomach
20	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:247460600-247463600	Strong transcription	A549	lung
22	chr1:247460800-247462800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:247460800-247463000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:247460800-247463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:247460800-247463000	Weak transcription	HepG2	liver
26	chr1:247460800-247463200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:247460800-247464800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:247460800-247471600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:247460800-247474200	Strong transcription	Brain Germinal Matrix	brain
30	chr1:247460800-247474800	Strong transcription	Brain Cingulate Gyrus	brain
31	chr1:247460800-247476200	Weak transcription	HMEC	breast
32	chr1:247460800-247479800	Strong transcription	Fetal Brain Female	brain
33	chr1:247460800-247481000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:247460800-247491800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:247461000-247464000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:247461000-247468600	Strong transcription	Right Ventricle	heart
38	chr1:247461000-247469000	Strong transcription	Brain Anterior Caudate	brain
39	chr1:247461000-247475400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:247461000-247485400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:247461200-247465800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:247461200-247466000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:247461200-247473600	Weak transcription	HUVEC	blood vessel
44	chr1:247461200-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:247461200-247488200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:247461400-247463600	Weak transcription	Colonic Mucosa	Colon
47	chr1:247461400-247471600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:247461400-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:247461600-247463200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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