Variant report

Variant	rs6502615
Chromosome Location	chr17:17612023-17612024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17610633..17612841-chr17:17617873..17620812,2	K562	blood:
2	chr17:17583721..17585944-chr17:17610998..17613902,2	K562	blood:
3	chr17:17606494..17609263-chr17:17609958..17614352,4	K562	blood:

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12940014	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs12942059	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12945601	0.92[JPT][hapmap]
rs2001884	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4496218	0.89[CEU][hapmap]
rs4925092	0.85[CEU][hapmap]
rs4925093	0.85[CEU][hapmap]
rs4925094	0.85[CEU][hapmap]
rs4925102	0.83[AMR][1000 genomes]
rs4925104	0.89[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs4925105	0.89[CEU][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes]
rs4925108	0.92[JPT][hapmap]
rs6502613	0.89[CEU][hapmap]
rs7208561	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224617	0.89[CEU][hapmap]
rs7224739	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8065154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941444	0.92[JPT][hapmap]
rs9897309	0.89[CEU][hapmap];0.90[CHD][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes]
rs9897596	0.82[AMR][1000 genomes]
rs9899445	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910411	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
6	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
7	nsv907753	chr17:17573539-17747289	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv907754	chr17:17573539-17782404	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv1061126	chr17:17578826-17803194	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv543238	chr17:17578826-17803194	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
11	nsv833385	chr17:17594037-17765578	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
12	nsv1058884	chr17:17594370-17803194	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
13	nsv543240	chr17:17594370-17803194	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv543241	chr17:17596222-17703059	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1064176	chr17:17596222-17803194	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv543242	chr17:17596222-17803194	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv1062361	chr17:17598407-17746899	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
18	nsv543243	chr17:17598407-17746899	Genic enhancers Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6502615	CDRT4	cis	cerebellum	SCAN
rs6502615	TOM1L2	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17599200-17615600	Weak transcription	Primary B cells from cord blood	blood
2	chr17:17599400-17617200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr17:17599400-17617400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:17599600-17612400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr17:17600400-17614800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr17:17601400-17617600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:17602800-17613200	Weak transcription	Hela-S3	cervix
8	chr17:17602800-17613400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:17602800-17613600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr17:17603600-17613800	Weak transcription	HSMM	muscle
11	chr17:17604200-17613200	Weak transcription	HMEC	breast
12	chr17:17604200-17614000	Weak transcription	Small Intestine	intestine
13	chr17:17604800-17614600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr17:17604800-17614600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr17:17605600-17614400	Weak transcription	Brain Substantia Nigra	brain
16	chr17:17606000-17612800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:17606000-17613600	Weak transcription	Brain Angular Gyrus	brain
18	chr17:17606000-17613600	Weak transcription	Fetal Brain Male	brain
19	chr17:17606400-17614600	Weak transcription	Fetal Kidney	kidney
20	chr17:17606400-17615600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr17:17606600-17613200	Weak transcription	Colonic Mucosa	Colon
22	chr17:17606600-17613200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr17:17606600-17613400	Weak transcription	Colon Smooth Muscle	Colon
24	chr17:17606800-17612400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr17:17606800-17613800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr17:17607000-17612200	Weak transcription	Fetal Thymus	thymus
27	chr17:17607000-17613400	Weak transcription	NH-A	brain
28	chr17:17607200-17612600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr17:17607200-17614200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr17:17607400-17612400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:17607400-17613200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr17:17607400-17614000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:17607400-17614600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr17:17607600-17613000	Weak transcription	Brain Hippocampus Middle	brain
35	chr17:17607600-17613400	Weak transcription	Fetal Heart	heart
36	chr17:17607600-17613600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:17608000-17612400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr17:17608000-17613600	Weak transcription	Ovary	ovary
39	chr17:17608000-17614400	Weak transcription	Brain Germinal Matrix	brain
40	chr17:17608400-17613800	Weak transcription	Right Atrium	heart
41	chr17:17608600-17613200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr17:17608600-17613800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr17:17608600-17614600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr17:17608600-17620400	Weak transcription	Dnd41	blood
45	chr17:17608800-17615600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:17609000-17612800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr17:17609200-17616600	Enhancers	Fetal Intestine Large	intestine
48	chr17:17609400-17614200	Genic enhancers	Fetal Intestine Small	intestine
49	chr17:17609400-17614400	Enhancers	HepG2	liver
50	chr17:17609400-17618200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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