Variant report

Variant	rs6115202
Chromosome Location	chr20:25497538-25497539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25491958..25494931-chr20:25496004..25498993,2	MCF-7	breast:
2	chr20:25476872..25479818-chr20:25496364..25499002,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11699872	0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11700213	0.95[ASN][1000 genomes]
rs11700338	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11905437	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs12480853	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12481037	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs12481409	0.89[ASN][1000 genomes]
rs12625157	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12625748	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs16987806	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs17244452	0.86[YRI][hapmap]
rs1888037	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2050097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2072976	0.87[ASN][1000 genomes]
rs2274890	0.91[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs2281212	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3736720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3764694	0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4815438	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs55792313	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56238023	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6037190	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6050690	0.87[CHB][hapmap]
rs6107050	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6115193	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs6115200	0.95[LWK][hapmap]
rs6115208	0.84[ASW][hapmap];0.86[YRI][hapmap]
rs6115214	0.95[LWK][hapmap]
rs6115218	0.87[LWK][hapmap]
rs6115223	0.86[YRI][hapmap]
rs6115227	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6115241	0.83[CHB][hapmap]
rs6115248	0.84[ASW][hapmap];0.86[YRI][hapmap]
rs6138588	0.95[LWK][hapmap]
rs66807280	0.88[ASN][1000 genomes]
rs7272126	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs73109499	0.99[ASN][1000 genomes]
rs73597807	0.81[ASN][1000 genomes]
rs73597824	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9305141	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6115202	ABHD12	cis	Frontal Cortex	GTEx
rs6115202	ABHD12	cis	brain	seeQTL
rs6115202	NINL	cis	parietal	SCAN
rs6115202	GINS1	cis	parietal	SCAN
rs6115202	C20orf22	cis	multi-tissue	Pritchard
rs6115202	KIAA0980	cis	multi-tissue	Pritchard
rs6115202	ABHD12	cis	cerebellum	SCAN
rs6115202	ABHD12	cis	Cerebellum	GTEx
rs6115202	PYGB	cis	cerebellum	SCAN
rs6115202	PYGB	cis	multi-tissue	Pritchard
rs6115202	ABHD12	cis	lymphoblastoid	seeQTL
rs6115202	ENTPD6	cis	cerebellum	SCAN
rs6115202	PYGB	cis	Skin Sun Exposed Lower leg	GTEx
rs6115202	ABHD12	trans	brain	seeQTL
rs6115202	ABHD12	cis	Temporal Cortex	GTEx
rs6115202	NINL	cis	cerebellum	SCAN
rs6115202	HDHD4	cis	multi-tissue	Pritchard
rs6115202	ABHD12	cis	Brain Pons	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25475400-25498000	Weak transcription	Right Ventricle	heart
2	chr20:25485800-25498600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:25487200-25498200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr20:25489400-25505800	Weak transcription	NHDF-Ad	bronchial
5	chr20:25491200-25506200	Weak transcription	NHLF	lung
6	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
7	chr20:25493400-25499000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr20:25493600-25498200	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
10	chr20:25494000-25499000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:25494000-25502000	ZNF genes & repeats	Dnd41	blood
12	chr20:25494200-25498200	ZNF genes & repeats	Thymus	Thymus
13	chr20:25494400-25497600	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr20:25494400-25499000	ZNF genes & repeats	Brain Germinal Matrix	brain
15	chr20:25494400-25499000	ZNF genes & repeats	Fetal Brain Female	brain
16	chr20:25494400-25499200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr20:25494600-25497600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr20:25494600-25497600	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr20:25494600-25498000	ZNF genes & repeats	HepG2	liver
20	chr20:25494600-25498200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr20:25494600-25498200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
22	chr20:25494600-25498200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr20:25494600-25498200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
24	chr20:25494800-25497600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
25	chr20:25494800-25497600	ZNF genes & repeats	A549	lung
26	chr20:25494800-25497800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr20:25494800-25498000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr20:25494800-25498200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
29	chr20:25494800-25498200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr20:25494800-25498200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr20:25494800-25498200	ZNF genes & repeats	Fetal Stomach	stomach
32	chr20:25495000-25497800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr20:25495000-25498200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr20:25495200-25498000	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr20:25495200-25498200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr20:25495200-25498200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
37	chr20:25495200-25498200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:25495200-25498200	ZNF genes & repeats	Fetal Thymus	thymus
39	chr20:25495600-25504800	Weak transcription	Osteobl	bone
40	chr20:25495800-25497800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr20:25495800-25498200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr20:25495800-25498200	Strong transcription	Adipose Nuclei	Adipose
43	chr20:25495800-25502200	Weak transcription	Stomach Mucosa	stomach
44	chr20:25495800-25506400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr20:25496000-25498000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:25496000-25498200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr20:25496000-25498200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr20:25496000-25498400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr20:25496000-25512400	Weak transcription	Brain Angular Gyrus	brain

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